Ben Bolstad
| Snapshot Date: 2025-11-18 13:40 -0500 (Tue, 18 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/BufferedMatrix |
| git_branch: devel |
| git_last_commit: ecdbf23 |
| git_last_commit_date: 2025-10-29 09:58:55 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-19 10:13 -0500 (Wed, 19 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4827 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4600 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4564 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 251/2325 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BufferedMatrix 1.75.0 (landing page) Ben Bolstad
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
|
To the developers/maintainers of the BufferedMatrix package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BufferedMatrix.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BufferedMatrix |
| Version: 1.75.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BufferedMatrix_1.75.0.tar.gz |
| StartedAt: 2025-11-18 19:48:17 -0500 (Tue, 18 Nov 2025) |
| EndedAt: 2025-11-18 19:49:13 -0500 (Tue, 18 Nov 2025) |
| EllapsedTime: 55.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BufferedMatrix_1.75.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck’
* using R Under development (unstable) (2025-10-21 r88958)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BufferedMatrix/DESCRIPTION’ ... OK
* this is package ‘BufferedMatrix’ version ‘1.75.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BufferedMatrix’ can be installed ... WARNING
Found the following significant warnings:
doubleBufferedMatrix.c:1580:7: warning: logical not is only applied to the left hand side of this bitwise operator [-Wlogical-not-parentheses]
See ‘/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) BufferedMatrix-class.Rd:209: Lost braces; missing escapes or markup?
209 | $x^{power}$ elementwise of the matrix
| ^
prepare_Rd: createBufferedMatrix.Rd:26: Dropping empty section \keyword
prepare_Rd: createBufferedMatrix.Rd:17-18: Dropping empty section \details
prepare_Rd: createBufferedMatrix.Rd:15-16: Dropping empty section \value
prepare_Rd: createBufferedMatrix.Rd:19-20: Dropping empty section \references
prepare_Rd: createBufferedMatrix.Rd:21-22: Dropping empty section \seealso
prepare_Rd: createBufferedMatrix.Rd:23-24: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... INFO
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘Rcodetesting.R’
Running ‘c_code_level_tests.R’
Running ‘objectTesting.R’
Running ‘rawCalltesting.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 1 NOTE
See
‘/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/00check.log’
for details.
BufferedMatrix.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BufferedMatrix
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library’
* installing *source* package ‘BufferedMatrix’ ...
** this is package ‘BufferedMatrix’ version ‘1.75.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using SDK: ‘MacOSX11.3.1.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RBufferedMatrix.c -o RBufferedMatrix.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c doubleBufferedMatrix.c -o doubleBufferedMatrix.o
doubleBufferedMatrix.c:1580:7: warning: logical not is only applied to the left hand side of this bitwise operator [-Wlogical-not-parentheses]
if (!(Matrix->readonly) & setting){
^ ~
doubleBufferedMatrix.c:1580:7: note: add parentheses after the '!' to evaluate the bitwise operator first
if (!(Matrix->readonly) & setting){
^
( )
doubleBufferedMatrix.c:1580:7: note: add parentheses around left hand side expression to silence this warning
if (!(Matrix->readonly) & setting){
^
( )
doubleBufferedMatrix.c:3327:12: warning: unused function 'sort_double' [-Wunused-function]
static int sort_double(const double *a1,const double *a2){
^
2 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c doubleBufferedMatrix_C_tests.c -o doubleBufferedMatrix_C_tests.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init_package.c -o init_package.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o BufferedMatrix.so RBufferedMatrix.o doubleBufferedMatrix.o doubleBufferedMatrix_C_tests.o init_package.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/00LOCK-BufferedMatrix/00new/BufferedMatrix/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘rowMeans’ in package ‘BufferedMatrix’
Creating a new generic function for ‘rowSums’ in package ‘BufferedMatrix’
Creating a new generic function for ‘colMeans’ in package ‘BufferedMatrix’
Creating a new generic function for ‘colSums’ in package ‘BufferedMatrix’
Creating a generic function for ‘ncol’ from package ‘base’ in package ‘BufferedMatrix’
Creating a generic function for ‘nrow’ from package ‘base’ in package ‘BufferedMatrix’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BufferedMatrix)
BufferedMatrix.Rcheck/tests/c_code_level_tests.Rout
R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix", "BufferedMatrix", .libPaths());.C("dbm_c_tester",integer(1))
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
Adding Additional Column
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
0.000000 1.000000 2.000000 3.000000 4.000000 0.000000
1.000000 2.000000 3.000000 4.000000 5.000000 0.000000
2.000000 3.000000 4.000000 5.000000 6.000000 0.000000
3.000000 4.000000 5.000000 6.000000 7.000000 0.000000
4.000000 5.000000 6.000000 7.000000 8.000000 0.000000
Reassigning values
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Resizing Buffers
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 3
Buffer Cols: 3
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Activating Row Buffer
In row mode: 1
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Squaring Last Column
1.000000 6.000000 11.000000 16.000000 21.000000 676.000000
2.000000 7.000000 12.000000 17.000000 22.000000 729.000000
3.000000 8.000000 13.000000 18.000000 23.000000 784.000000
4.000000 9.000000 14.000000 19.000000 24.000000 841.000000
5.000000 10.000000 15.000000 20.000000 25.000000 900.000000
Square rooting Last Row, then turing off Row Buffer
In row mode: 0
Checking on value that should be not be in column buffer2.236068
1.000000 6.000000 11.000000 16.000000 21.000000 676.000000
2.000000 7.000000 12.000000 17.000000 22.000000 729.000000
3.000000 8.000000 13.000000 18.000000 23.000000 784.000000
4.000000 9.000000 14.000000 19.000000 24.000000 841.000000
2.236068 3.162278 3.872983 4.472136 5.000000 30.000000
Single Indexing. Assign each value its square
1.000000 36.000000 121.000000 256.000000 441.000000 676.000000
4.000000 49.000000 144.000000 289.000000 484.000000 729.000000
9.000000 64.000000 169.000000 324.000000 529.000000 784.000000
16.000000 81.000000 196.000000 361.000000 576.000000 841.000000
25.000000 100.000000 225.000000 400.000000 625.000000 900.000000
Resizing Buffers Smaller
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
1.000000 36.000000 121.000000 256.000000 441.000000 676.000000
4.000000 49.000000 144.000000 289.000000 484.000000 729.000000
9.000000 64.000000 169.000000 324.000000 529.000000 784.000000
16.000000 81.000000 196.000000 361.000000 576.000000 841.000000
25.000000 100.000000 225.000000 400.000000 625.000000 900.000000
Activating Row Mode.
Resizing Buffers
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
Activating ReadOnly Mode.
The results of assignment is: 0
Printing matrix reversed.
900.000000 625.000000 400.000000 225.000000 100.000000 25.000000
841.000000 576.000000 361.000000 196.000000 81.000000 16.000000
784.000000 529.000000 324.000000 169.000000 64.000000 9.000000
729.000000 484.000000 289.000000 144.000000 49.000000 -30.000000
676.000000 441.000000 256.000000 121.000000 -20.000000 -10.000000
[[1]]
[1] 0
>
> proc.time()
user system elapsed
0.325 0.155 0.499
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
>
> ### this is used to control how many repetitions in something below
> ### higher values result in more checks.
> nreps <-100 ##20000
>
>
> ## test creation and some simple assignments and subsetting operations
>
> ## first on single elements
> tmp <- createBufferedMatrix(1000,10)
>
> tmp[10,5]
[1] 0
> tmp[10,5] <- 10
> tmp[10,5]
[1] 10
> tmp[10,5] <- 12.445
> tmp[10,5]
[1] 12.445
>
>
>
> ## now testing accessing multiple elements
> tmp2 <- createBufferedMatrix(10,20)
>
>
> tmp2[3,1] <- 51.34
> tmp2[9,2] <- 9.87654
> tmp2[,1:2]
[,1] [,2]
[1,] 0.00 0.00000
[2,] 0.00 0.00000
[3,] 51.34 0.00000
[4,] 0.00 0.00000
[5,] 0.00 0.00000
[6,] 0.00 0.00000
[7,] 0.00 0.00000
[8,] 0.00 0.00000
[9,] 0.00 9.87654
[10,] 0.00 0.00000
> tmp2[,-(3:20)]
[,1] [,2]
[1,] 0.00 0.00000
[2,] 0.00 0.00000
[3,] 51.34 0.00000
[4,] 0.00 0.00000
[5,] 0.00 0.00000
[6,] 0.00 0.00000
[7,] 0.00 0.00000
[8,] 0.00 0.00000
[9,] 0.00 9.87654
[10,] 0.00 0.00000
> tmp2[3,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 51.34 0 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
[1,] 0 0 0 0 0 0 0
> tmp2[-3,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[2,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[3,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[4,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[5,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[6,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[7,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[8,] 0 9.87654 0 0 0 0 0 0 0 0 0 0 0
[9,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
[1,] 0 0 0 0 0 0 0
[2,] 0 0 0 0 0 0 0
[3,] 0 0 0 0 0 0 0
[4,] 0 0 0 0 0 0 0
[5,] 0 0 0 0 0 0 0
[6,] 0 0 0 0 0 0 0
[7,] 0 0 0 0 0 0 0
[8,] 0 0 0 0 0 0 0
[9,] 0 0 0 0 0 0 0
> tmp2[2,1:3]
[,1] [,2] [,3]
[1,] 0 0 0
> tmp2[3:9,1:3]
[,1] [,2] [,3]
[1,] 51.34 0.00000 0
[2,] 0.00 0.00000 0
[3,] 0.00 0.00000 0
[4,] 0.00 0.00000 0
[5,] 0.00 0.00000 0
[6,] 0.00 0.00000 0
[7,] 0.00 9.87654 0
> tmp2[-4,-4]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[2,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[3,] 51.34 0.00000 0 0 0 0 0 0 0 0 0 0 0
[4,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[5,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[6,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[7,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[8,] 0.00 9.87654 0 0 0 0 0 0 0 0 0 0 0
[9,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19]
[1,] 0 0 0 0 0 0
[2,] 0 0 0 0 0 0
[3,] 0 0 0 0 0 0
[4,] 0 0 0 0 0 0
[5,] 0 0 0 0 0 0
[6,] 0 0 0 0 0 0
[7,] 0 0 0 0 0 0
[8,] 0 0 0 0 0 0
[9,] 0 0 0 0 0 0
>
> ## now testing accessing/assigning multiple elements
> tmp3 <- createBufferedMatrix(10,10)
>
> for (i in 1:10){
+ for (j in 1:10){
+ tmp3[i,j] <- (j-1)*10 + i
+ }
+ }
>
> tmp3[2:4,2:4]
[,1] [,2] [,3]
[1,] 12 22 32
[2,] 13 23 33
[3,] 14 24 34
> tmp3[c(-10),c(2:4,2:4,10,1,2,1:10,10:1)]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 11 21 31 11 21 31 91 1 11 1 11 21 31
[2,] 12 22 32 12 22 32 92 2 12 2 12 22 32
[3,] 13 23 33 13 23 33 93 3 13 3 13 23 33
[4,] 14 24 34 14 24 34 94 4 14 4 14 24 34
[5,] 15 25 35 15 25 35 95 5 15 5 15 25 35
[6,] 16 26 36 16 26 36 96 6 16 6 16 26 36
[7,] 17 27 37 17 27 37 97 7 17 7 17 27 37
[8,] 18 28 38 18 28 38 98 8 18 8 18 28 38
[9,] 19 29 39 19 29 39 99 9 19 9 19 29 39
[,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25]
[1,] 41 51 61 71 81 91 91 81 71 61 51 41
[2,] 42 52 62 72 82 92 92 82 72 62 52 42
[3,] 43 53 63 73 83 93 93 83 73 63 53 43
[4,] 44 54 64 74 84 94 94 84 74 64 54 44
[5,] 45 55 65 75 85 95 95 85 75 65 55 45
[6,] 46 56 66 76 86 96 96 86 76 66 56 46
[7,] 47 57 67 77 87 97 97 87 77 67 57 47
[8,] 48 58 68 78 88 98 98 88 78 68 58 48
[9,] 49 59 69 79 89 99 99 89 79 69 59 49
[,26] [,27] [,28] [,29]
[1,] 31 21 11 1
[2,] 32 22 12 2
[3,] 33 23 13 3
[4,] 34 24 14 4
[5,] 35 25 15 5
[6,] 36 26 16 6
[7,] 37 27 17 7
[8,] 38 28 18 8
[9,] 39 29 19 9
> tmp3[-c(1:5),-c(6:10)]
[,1] [,2] [,3] [,4] [,5]
[1,] 6 16 26 36 46
[2,] 7 17 27 37 47
[3,] 8 18 28 38 48
[4,] 9 19 29 39 49
[5,] 10 20 30 40 50
>
> ## assignment of whole columns
> tmp3[,1] <- c(1:10*100.0)
> tmp3[,1:2] <- tmp3[,1:2]*100
> tmp3[,1:2] <- tmp3[,2:1]
> tmp3[,1:2]
[,1] [,2]
[1,] 1100 1e+04
[2,] 1200 2e+04
[3,] 1300 3e+04
[4,] 1400 4e+04
[5,] 1500 5e+04
[6,] 1600 6e+04
[7,] 1700 7e+04
[8,] 1800 8e+04
[9,] 1900 9e+04
[10,] 2000 1e+05
>
>
> tmp3[,-1] <- tmp3[,1:9]
> tmp3[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1100 1100 1e+04 21 31 41 51 61 71 81
[2,] 1200 1200 2e+04 22 32 42 52 62 72 82
[3,] 1300 1300 3e+04 23 33 43 53 63 73 83
[4,] 1400 1400 4e+04 24 34 44 54 64 74 84
[5,] 1500 1500 5e+04 25 35 45 55 65 75 85
[6,] 1600 1600 6e+04 26 36 46 56 66 76 86
[7,] 1700 1700 7e+04 27 37 47 57 67 77 87
[8,] 1800 1800 8e+04 28 38 48 58 68 78 88
[9,] 1900 1900 9e+04 29 39 49 59 69 79 89
[10,] 2000 2000 1e+05 30 40 50 60 70 80 90
>
> tmp3[,1:2] <- rep(1,10)
> tmp3[,1:2] <- rep(1,20)
> tmp3[,1:2] <- matrix(c(1:5),1,5)
>
> tmp3[,-c(1:8)] <- matrix(c(1:5),1,5)
>
> tmp3[1,] <- 1:10
> tmp3[1,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
> tmp3[-1,] <- c(1,2)
> tmp3[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
[2,] 1 2 1 2 1 2 1 2 1 2
[3,] 2 1 2 1 2 1 2 1 2 1
[4,] 1 2 1 2 1 2 1 2 1 2
[5,] 2 1 2 1 2 1 2 1 2 1
[6,] 1 2 1 2 1 2 1 2 1 2
[7,] 2 1 2 1 2 1 2 1 2 1
[8,] 1 2 1 2 1 2 1 2 1 2
[9,] 2 1 2 1 2 1 2 1 2 1
[10,] 1 2 1 2 1 2 1 2 1 2
> tmp3[-c(1:8),] <- matrix(c(1:5),1,5)
> tmp3[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
[2,] 1 2 1 2 1 2 1 2 1 2
[3,] 2 1 2 1 2 1 2 1 2 1
[4,] 1 2 1 2 1 2 1 2 1 2
[5,] 2 1 2 1 2 1 2 1 2 1
[6,] 1 2 1 2 1 2 1 2 1 2
[7,] 2 1 2 1 2 1 2 1 2 1
[8,] 1 2 1 2 1 2 1 2 1 2
[9,] 1 3 5 2 4 1 3 5 2 4
[10,] 2 4 1 3 5 2 4 1 3 5
>
>
> tmp3[1:2,1:2] <- 5555.04
> tmp3[-(1:2),1:2] <- 1234.56789
>
>
>
> ## testing accessors for the directory and prefix
> directory(tmp3)
[1] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests"
> prefix(tmp3)
[1] "BM"
>
> ## testing if we can remove these objects
> rm(tmp, tmp2, tmp3)
> gc()
used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
Ncells 481268 25.8 1058102 56.6 NA 633897 33.9
Vcells 891509 6.9 8388608 64.0 98304 2110436 16.2
>
>
>
>
> ##
> ## checking reads
> ##
>
> tmp2 <- createBufferedMatrix(10,20)
>
> test.sample <- rnorm(10*20)
>
> tmp2[1:10,1:20] <- test.sample
>
> test.matrix <- matrix(test.sample,10,20)
>
> ## testing reads
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ which.col <- sample(1:20,1)
+ if (tmp2[which.row,which.col] != test.matrix[which.row,which.col]){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> date()
[1] "Tue Nov 18 19:48:45 2025"
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
> date()
[1] "Tue Nov 18 19:48:45 2025"
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,which.col] == test.matrix[which.row,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
>
>
> RowMode(tmp2)
<pointer: 0x600003f38000>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ which.col <- sample(1:20,1)
+ if (tmp2[which.row,which.col] != test.matrix[which.row,which.col]){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> date()
[1] "Tue Nov 18 19:48:50 2025"
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[which.row,which.col] == test.matrix[which.row,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
> date()
[1] "Tue Nov 18 19:48:52 2025"
>
> ColMode(tmp2)
<pointer: 0x600003f38000>
>
>
>
> ### Now testing assignments
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+
+ new.data <- rnorm(20)
+ tmp2[which.row,] <- new.data
+ test.matrix[which.row,] <- new.data
+ if (rep > 1){
+ if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ new.data <- rnorm(10)
+ tmp2[,which.col] <- new.data
+ test.matrix[,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.col <- which.col
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ new.data <- matrix(rnorm(50),5,10)
+ tmp2[,which.col] <- new.data
+ test.matrix[,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.col <- which.col
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ new.data <- matrix(rnorm(50),5,10)
+ tmp2[which.row,] <- new.data
+ test.matrix[which.row,]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:20,5,replace=TRUE)
+ new.data <- matrix(rnorm(25),5,5)
+ tmp2[which.row,which.col] <- new.data
+ test.matrix[which.row,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[prev.row,prev.col] == test.matrix[prev.row,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+ prev.col <- which.col
+ }
>
>
>
>
> ###
> ###
> ### testing some more functions
> ###
>
>
>
> ## duplication function
> tmp5 <- duplicate(tmp2)
>
> # making sure really did copy everything.
> tmp5[1,1] <- tmp5[1,1] +100.00
>
> if (tmp5[1,1] == tmp2[1,1]){
+ stop("Problem with duplication")
+ }
>
>
>
>
> ### testing elementwise applying of functions
>
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 98.7557458 -0.3702357 0.9821002 -0.08566931
[2,] 0.6448573 1.0547075 -0.8762210 0.21424688
[3,] -1.3243470 -1.1857782 2.2474504 -0.35108174
[4,] 0.3413920 -0.5750576 -1.0998803 2.55617972
> ewApply(tmp5,abs)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 98.7557458 0.3702357 0.9821002 0.08566931
[2,] 0.6448573 1.0547075 0.8762210 0.21424688
[3,] 1.3243470 1.1857782 2.2474504 0.35108174
[4,] 0.3413920 0.5750576 1.0998803 2.55617972
> ewApply(tmp5,sqrt)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 9.9375926 0.6084700 0.9910097 0.2926932
[2,] 0.8030301 1.0269895 0.9360668 0.4628681
[3,] 1.1508027 1.0889344 1.4991499 0.5925215
[4,] 0.5842876 0.7583255 1.0487518 1.5988057
>
> my.function <- function(x,power){
+ (x+5)^power
+ }
>
> ewApply(tmp5,my.function,power=2)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 223.13167 31.45494 35.89220 28.01260
[2,] 33.67516 36.32460 35.23689 29.84293
[3,] 37.83237 37.07512 42.23895 31.27630
[4,] 31.18427 33.15831 36.58740 43.54424
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x600003f580c0>
> exp(tmp5)
<pointer: 0x600003f580c0>
> log(tmp5,2)
<pointer: 0x600003f580c0>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 464.4193
> Min(tmp5)
[1] 52.83235
> mean(tmp5)
[1] 73.27864
> Sum(tmp5)
[1] 14655.73
> Var(tmp5)
[1] 833.0722
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 91.17798 70.69753 74.95896 72.72412 69.26357 73.27135 69.87201 73.39037
[9] 69.34682 68.08372
> rowSums(tmp5)
[1] 1823.560 1413.951 1499.179 1454.482 1385.271 1465.427 1397.440 1467.807
[9] 1386.936 1361.674
> rowVars(tmp5)
[1] 7770.28522 46.75785 42.42443 86.91004 47.88860 69.51830
[7] 37.49294 69.94229 63.16842 69.51078
> rowSd(tmp5)
[1] 88.149221 6.837971 6.513404 9.322556 6.920159 8.337763 6.123148
[8] 8.363151 7.947856 8.337312
> rowMax(tmp5)
[1] 464.41934 79.95694 87.91484 90.63162 85.11999 96.64589 80.80496
[8] 90.46441 82.98526 88.19178
> rowMin(tmp5)
[1] 58.30456 57.19882 60.26057 56.42902 54.13022 60.93984 58.67219 57.08543
[9] 52.83235 53.68715
>
> colMeans(tmp5)
[1] 111.73131 69.85221 73.59309 71.42272 70.64064 69.01415 70.06267
[8] 72.85809 68.00985 70.99086 69.68480 75.54482 70.98041 70.52409
[15] 71.38763 70.98202 71.52459 69.35465 74.18047 73.23377
> colSums(tmp5)
[1] 1117.3131 698.5221 735.9309 714.2272 706.4064 690.1415 700.6267
[8] 728.5809 680.0985 709.9086 696.8480 755.4482 709.8041 705.2409
[15] 713.8763 709.8202 715.2459 693.5465 741.8047 732.3377
> colVars(tmp5)
[1] 15409.80122 31.27329 66.31150 97.85054 91.59920 38.58618
[7] 88.19834 59.35278 61.96418 58.35516 66.15220 82.28695
[13] 29.68948 126.13885 53.69884 38.26321 55.86641 51.77588
[19] 46.51966 64.67823
> colSd(tmp5)
[1] 124.136220 5.592253 8.143187 9.891943 9.570747 6.211777
[7] 9.391397 7.704076 7.871733 7.639055 8.133401 9.071215
[13] 5.448805 11.231155 7.327949 6.185726 7.474383 7.195546
[19] 6.820532 8.042277
> colMax(tmp5)
[1] 464.41934 78.24822 87.91484 90.63162 80.80496 78.44697 87.13999
[8] 90.12795 78.73820 83.80986 85.11999 88.19178 79.28155 96.64589
[15] 81.12454 79.53836 84.19689 80.37867 83.88009 90.46441
> colMin(tmp5)
[1] 63.12053 60.52082 60.62726 58.30456 53.68715 57.08543 58.67219 60.12069
[9] 56.42902 57.19882 52.83235 58.95525 62.05489 56.20318 58.64874 60.93984
[17] 60.26057 58.52312 63.29606 64.50402
>
>
> ### setting a random element to NA and then testing with na.rm=TRUE or na.rm=FALSE (The default)
>
>
> which.row <- sample(1:10,1,replace=TRUE)
> which.col <- sample(1:20,1,replace=TRUE)
>
> tmp5[which.row,which.col] <- NA
>
> Max(tmp5)
[1] NA
> Min(tmp5)
[1] NA
> mean(tmp5)
[1] NA
> Sum(tmp5)
[1] NA
> Var(tmp5)
[1] NA
>
> rowMeans(tmp5)
[1] 91.17798 70.69753 74.95896 72.72412 69.26357 73.27135 69.87201 NA
[9] 69.34682 68.08372
> rowSums(tmp5)
[1] 1823.560 1413.951 1499.179 1454.482 1385.271 1465.427 1397.440 NA
[9] 1386.936 1361.674
> rowVars(tmp5)
[1] 7770.28522 46.75785 42.42443 86.91004 47.88860 69.51830
[7] 37.49294 70.99305 63.16842 69.51078
> rowSd(tmp5)
[1] 88.149221 6.837971 6.513404 9.322556 6.920159 8.337763 6.123148
[8] 8.425737 7.947856 8.337312
> rowMax(tmp5)
[1] 464.41934 79.95694 87.91484 90.63162 85.11999 96.64589 80.80496
[8] NA 82.98526 88.19178
> rowMin(tmp5)
[1] 58.30456 57.19882 60.26057 56.42902 54.13022 60.93984 58.67219 NA
[9] 52.83235 53.68715
>
> colMeans(tmp5)
[1] 111.73131 69.85221 73.59309 71.42272 70.64064 69.01415 70.06267
[8] 72.85809 68.00985 70.99086 69.68480 75.54482 70.98041 70.52409
[15] NA 70.98202 71.52459 69.35465 74.18047 73.23377
> colSums(tmp5)
[1] 1117.3131 698.5221 735.9309 714.2272 706.4064 690.1415 700.6267
[8] 728.5809 680.0985 709.9086 696.8480 755.4482 709.8041 705.2409
[15] NA 709.8202 715.2459 693.5465 741.8047 732.3377
> colVars(tmp5)
[1] 15409.80122 31.27329 66.31150 97.85054 91.59920 38.58618
[7] 88.19834 59.35278 61.96418 58.35516 66.15220 82.28695
[13] 29.68948 126.13885 NA 38.26321 55.86641 51.77588
[19] 46.51966 64.67823
> colSd(tmp5)
[1] 124.136220 5.592253 8.143187 9.891943 9.570747 6.211777
[7] 9.391397 7.704076 7.871733 7.639055 8.133401 9.071215
[13] 5.448805 11.231155 NA 6.185726 7.474383 7.195546
[19] 6.820532 8.042277
> colMax(tmp5)
[1] 464.41934 78.24822 87.91484 90.63162 80.80496 78.44697 87.13999
[8] 90.12795 78.73820 83.80986 85.11999 88.19178 79.28155 96.64589
[15] NA 79.53836 84.19689 80.37867 83.88009 90.46441
> colMin(tmp5)
[1] 63.12053 60.52082 60.62726 58.30456 53.68715 57.08543 58.67219 60.12069
[9] 56.42902 57.19882 52.83235 58.95525 62.05489 56.20318 NA 60.93984
[17] 60.26057 58.52312 63.29606 64.50402
>
> Max(tmp5,na.rm=TRUE)
[1] 464.4193
> Min(tmp5,na.rm=TRUE)
[1] 52.83235
> mean(tmp5,na.rm=TRUE)
[1] 73.24309
> Sum(tmp5,na.rm=TRUE)
[1] 14575.38
> Var(tmp5,na.rm=TRUE)
[1] 837.0256
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 91.17798 70.69753 74.95896 72.72412 69.26357 73.27135 69.87201 73.02392
[9] 69.34682 68.08372
> rowSums(tmp5,na.rm=TRUE)
[1] 1823.560 1413.951 1499.179 1454.482 1385.271 1465.427 1397.440 1387.454
[9] 1386.936 1361.674
> rowVars(tmp5,na.rm=TRUE)
[1] 7770.28522 46.75785 42.42443 86.91004 47.88860 69.51830
[7] 37.49294 70.99305 63.16842 69.51078
> rowSd(tmp5,na.rm=TRUE)
[1] 88.149221 6.837971 6.513404 9.322556 6.920159 8.337763 6.123148
[8] 8.425737 7.947856 8.337312
> rowMax(tmp5,na.rm=TRUE)
[1] 464.41934 79.95694 87.91484 90.63162 85.11999 96.64589 80.80496
[8] 90.46441 82.98526 88.19178
> rowMin(tmp5,na.rm=TRUE)
[1] 58.30456 57.19882 60.26057 56.42902 54.13022 60.93984 58.67219 57.08543
[9] 52.83235 53.68715
>
> colMeans(tmp5,na.rm=TRUE)
[1] 111.73131 69.85221 73.59309 71.42272 70.64064 69.01415 70.06267
[8] 72.85809 68.00985 70.99086 69.68480 75.54482 70.98041 70.52409
[15] 70.39149 70.98202 71.52459 69.35465 74.18047 73.23377
> colSums(tmp5,na.rm=TRUE)
[1] 1117.3131 698.5221 735.9309 714.2272 706.4064 690.1415 700.6267
[8] 728.5809 680.0985 709.9086 696.8480 755.4482 709.8041 705.2409
[15] 633.5234 709.8202 715.2459 693.5465 741.8047 732.3377
> colVars(tmp5,na.rm=TRUE)
[1] 15409.80122 31.27329 66.31150 97.85054 91.59920 38.58618
[7] 88.19834 59.35278 61.96418 58.35516 66.15220 82.28695
[13] 29.68948 126.13885 49.24778 38.26321 55.86641 51.77588
[19] 46.51966 64.67823
> colSd(tmp5,na.rm=TRUE)
[1] 124.136220 5.592253 8.143187 9.891943 9.570747 6.211777
[7] 9.391397 7.704076 7.871733 7.639055 8.133401 9.071215
[13] 5.448805 11.231155 7.017676 6.185726 7.474383 7.195546
[19] 6.820532 8.042277
> colMax(tmp5,na.rm=TRUE)
[1] 464.41934 78.24822 87.91484 90.63162 80.80496 78.44697 87.13999
[8] 90.12795 78.73820 83.80986 85.11999 88.19178 79.28155 96.64589
[15] 81.12454 79.53836 84.19689 80.37867 83.88009 90.46441
> colMin(tmp5,na.rm=TRUE)
[1] 63.12053 60.52082 60.62726 58.30456 53.68715 57.08543 58.67219 60.12069
[9] 56.42902 57.19882 52.83235 58.95525 62.05489 56.20318 58.64874 60.93984
[17] 60.26057 58.52312 63.29606 64.50402
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 91.17798 70.69753 74.95896 72.72412 69.26357 73.27135 69.87201 NaN
[9] 69.34682 68.08372
> rowSums(tmp5,na.rm=TRUE)
[1] 1823.560 1413.951 1499.179 1454.482 1385.271 1465.427 1397.440 0.000
[9] 1386.936 1361.674
> rowVars(tmp5,na.rm=TRUE)
[1] 7770.28522 46.75785 42.42443 86.91004 47.88860 69.51830
[7] 37.49294 NA 63.16842 69.51078
> rowSd(tmp5,na.rm=TRUE)
[1] 88.149221 6.837971 6.513404 9.322556 6.920159 8.337763 6.123148
[8] NA 7.947856 8.337312
> rowMax(tmp5,na.rm=TRUE)
[1] 464.41934 79.95694 87.91484 90.63162 85.11999 96.64589 80.80496
[8] NA 82.98526 88.19178
> rowMin(tmp5,na.rm=TRUE)
[1] 58.30456 57.19882 60.26057 56.42902 54.13022 60.93984 58.67219 NA
[9] 52.83235 53.68715
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 114.34749 70.22188 74.15893 71.07013 69.77857 70.33957 70.07672
[8] 73.11006 67.52515 70.78954 68.95402 74.73014 70.50649 70.38956
[15] NaN 70.59256 72.67987 70.16683 74.17631 71.31925
> colSums(tmp5,na.rm=TRUE)
[1] 1029.1274 631.9969 667.4303 639.6312 628.0071 633.0561 630.6905
[8] 657.9906 607.7263 637.1059 620.5862 672.5713 634.5584 633.5061
[15] 0.0000 635.3330 654.1189 631.5014 667.5868 641.8733
> colVars(tmp5,na.rm=TRUE)
[1] 17259.02656 33.64513 70.99848 108.68324 94.68859 23.64634
[7] 99.22091 66.05762 67.06660 65.19362 68.41325 85.10613
[13] 30.87383 141.70262 NA 41.33968 47.83463 50.82707
[19] 52.33442 31.52757
> colSd(tmp5,na.rm=TRUE)
[1] 131.373614 5.800442 8.426060 10.425125 9.730806 4.862751
[7] 9.960969 8.127584 8.189420 8.074257 8.271230 9.225299
[13] 5.556422 11.903891 NA 6.429594 6.916258 7.129311
[19] 7.234254 5.614942
> colMax(tmp5,na.rm=TRUE)
[1] 464.41934 78.24822 87.91484 90.63162 80.80496 78.44697 87.13999
[8] 90.12795 78.73820 83.80986 85.11999 88.19178 79.28155 96.64589
[15] -Inf 79.53836 84.19689 80.37867 83.88009 82.30823
> colMin(tmp5,na.rm=TRUE)
[1] 63.12053 60.52082 60.62726 58.30456 53.68715 62.50630 58.67219 60.12069
[9] 56.42902 57.19882 52.83235 58.95525 62.05489 56.20318 Inf 60.93984
[17] 60.26057 58.52312 63.29606 64.50402
>
>
>
>
> copymatrix <- matrix(rnorm(200,150,15),10,20)
>
> tmp5[1:10,1:20] <- copymatrix
> which.row <- 3
> which.col <- 1
> cat(which.row," ",which.col,"\n")
3 1
> tmp5[which.row,which.col] <- NA
> copymatrix[which.row,which.col] <- NA
>
> rowVars(tmp5,na.rm=TRUE)
[1] 329.0917 176.4599 306.3059 247.2403 233.7156 342.8267 214.8643 273.1821
[9] 197.2522 287.7686
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 329.0917 176.4599 306.3059 247.2403 233.7156 342.8267 214.8643 273.1821
[9] 197.2522 287.7686
>
>
>
> copymatrix <- matrix(rnorm(200,150,15),10,20)
>
> tmp5[1:10,1:20] <- copymatrix
> which.row <- 1
> which.col <- 3
> cat(which.row," ",which.col,"\n")
1 3
> tmp5[which.row,which.col] <- NA
> copymatrix[which.row,which.col] <- NA
>
> colVars(tmp5,na.rm=TRUE)-apply(copymatrix,2,var,na.rm=TRUE)
[1] -5.684342e-14 1.136868e-13 -5.684342e-14 2.842171e-14 5.684342e-14
[6] -1.136868e-13 2.842171e-14 1.705303e-13 -1.136868e-13 -1.136868e-13
[11] 2.842171e-14 2.842171e-14 5.684342e-14 0.000000e+00 -7.105427e-15
[16] -2.842171e-14 0.000000e+00 -5.684342e-14 0.000000e+00 5.684342e-14
>
>
>
>
>
>
>
>
>
>
> ## making sure these things agree
> ##
> ## first when there is no NA
>
>
>
> agree.checks <- function(buff.matrix,r.matrix,err.tol=1e-10){
+
+ if (Max(buff.matrix,na.rm=TRUE) != max(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Max")
+ }
+
+
+ if (Min(buff.matrix,na.rm=TRUE) != min(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Min")
+ }
+
+
+ if (abs(Sum(buff.matrix,na.rm=TRUE)- sum(r.matrix,na.rm=TRUE)) > err.tol){
+
+ cat(Sum(buff.matrix,na.rm=TRUE),"\n")
+ cat(sum(r.matrix,na.rm=TRUE),"\n")
+ cat(Sum(buff.matrix,na.rm=TRUE) - sum(r.matrix,na.rm=TRUE),"\n")
+
+ stop("No agreement in Sum")
+ }
+
+ if (abs(mean(buff.matrix,na.rm=TRUE) - mean(r.matrix,na.rm=TRUE)) > err.tol){
+ stop("No agreement in mean")
+ }
+
+
+ if(abs(Var(buff.matrix,na.rm=TRUE) - var(as.vector(r.matrix),na.rm=TRUE)) > err.tol){
+ stop("No agreement in Var")
+ }
+
+
+
+ if(any(abs(rowMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,mean,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowMeans")
+ }
+
+
+ if(any(abs(colMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,mean,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colMeans")
+ }
+
+
+ if(any(abs(rowSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in rowSums")
+ }
+
+
+ if(any(abs(colSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colSums")
+ }
+
+ ### this is to get around the fact that R doesn't like to compute NA on an entire vector of NA when
+ ### computing variance
+ my.Var <- function(x,na.rm=FALSE){
+ if (all(is.na(x))){
+ return(NA)
+ } else {
+ var(x,na.rm=na.rm)
+ }
+
+ }
+
+ if(any(abs(rowVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(colVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(rowMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+ if(any(abs(colMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+
+ if(any(abs(rowMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+
+ if(any(abs(colMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+ if(any(abs(colMedians(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,median,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMedian")
+ }
+
+ if(any(abs(colRanges(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,range,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colRanges")
+ }
+
+
+
+ }
>
>
>
>
>
>
>
>
>
> for (rep in 1:20){
+ copymatrix <- matrix(rnorm(200,150,15),10,20)
+
+ tmp5[1:10,1:20] <- copymatrix
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ## now lets assign some NA values and check agreement
+
+ which.row <- sample(1:10,1,replace=TRUE)
+ which.col <- sample(1:20,1,replace=TRUE)
+
+ cat(which.row," ",which.col,"\n")
+
+ tmp5[which.row,which.col] <- NA
+ copymatrix[which.row,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ## make an entire row NA
+ tmp5[which.row,] <- NA
+ copymatrix[which.row,] <- NA
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ### also make an entire col NA
+ tmp5[,which.col] <- NA
+ copymatrix[,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ### now make 1 element non NA with NA in the rest of row and column
+
+ tmp5[which.row,which.col] <- rnorm(1,150,15)
+ copymatrix[which.row,which.col] <- tmp5[which.row,which.col]
+
+ agree.checks(tmp5,copymatrix)
+ }
2 20
1 9
5 16
6 3
9 13
2 3
9 4
9 17
3 14
8 17
6 7
9 4
3 4
3 12
8 9
8 13
3 14
4 12
10 6
9 15
There were 50 or more warnings (use warnings() to see the first 50)
>
>
> ### now test 1 by n and n by 1 matrix
>
>
> err.tol <- 1e-12
>
> rm(tmp5)
>
> dataset1 <- rnorm(100)
> dataset2 <- rnorm(100)
>
> tmp <- createBufferedMatrix(1,100)
> tmp[1,] <- dataset1
>
> tmp2 <- createBufferedMatrix(100,1)
> tmp2[,1] <- dataset2
>
>
>
>
>
> Max(tmp)
[1] 2.166788
> Min(tmp)
[1] -2.376345
> mean(tmp)
[1] -0.025797
> Sum(tmp)
[1] -2.5797
> Var(tmp)
[1] 0.9807334
>
> rowMeans(tmp)
[1] -0.025797
> rowSums(tmp)
[1] -2.5797
> rowVars(tmp)
[1] 0.9807334
> rowSd(tmp)
[1] 0.9903198
> rowMax(tmp)
[1] 2.166788
> rowMin(tmp)
[1] -2.376345
>
> colMeans(tmp)
[1] 0.702193186 -0.521402513 -0.775878314 0.222183990 -1.219836439
[6] 0.229487890 -1.344296329 -0.113096443 2.008796643 -0.952707912
[11] 2.152163492 0.716724724 -0.442323724 -0.121131820 1.934651509
[16] -0.585063822 -0.318226056 1.838997759 -0.123727871 0.224661361
[21] 0.539996312 0.148277850 0.196121471 -0.331367234 0.843580372
[26] -0.727632342 0.689264449 -0.263867790 0.517438408 -0.707217228
[31] -0.375451654 -1.437634975 0.978108581 -1.193986594 -1.454754954
[36] 1.367046007 -0.596025076 0.233078418 0.853249111 -0.285822360
[41] 0.486532999 1.186218849 0.632651896 -1.340651425 0.869184491
[46] -0.773460454 -0.897107003 1.625212131 0.101241576 -1.037235396
[51] -0.572655474 0.007281009 0.426810552 -0.518495434 0.114265920
[56] 0.142004273 0.493977482 -1.451855794 -0.626590737 0.049274366
[61] -0.706817575 -0.592081893 -0.094835348 -0.043309897 -0.264362552
[66] 0.029344977 0.975351465 0.036456554 -1.310646102 0.984447037
[71] -0.570136804 0.049756911 0.608219313 -0.080807626 1.453718122
[76] -1.139939311 0.322247520 -2.200206836 1.157057735 -0.794121780
[81] -0.168259537 -0.521008531 -1.521857333 -2.027906964 -2.376345057
[86] 0.573422964 0.887490994 1.087546388 2.166787802 -1.829151667
[91] 0.867032669 -0.845752571 -0.421414788 -1.543350626 1.582259892
[96] -0.156058239 0.398309319 -0.460206501 1.158191391 1.330062993
> colSums(tmp)
[1] 0.702193186 -0.521402513 -0.775878314 0.222183990 -1.219836439
[6] 0.229487890 -1.344296329 -0.113096443 2.008796643 -0.952707912
[11] 2.152163492 0.716724724 -0.442323724 -0.121131820 1.934651509
[16] -0.585063822 -0.318226056 1.838997759 -0.123727871 0.224661361
[21] 0.539996312 0.148277850 0.196121471 -0.331367234 0.843580372
[26] -0.727632342 0.689264449 -0.263867790 0.517438408 -0.707217228
[31] -0.375451654 -1.437634975 0.978108581 -1.193986594 -1.454754954
[36] 1.367046007 -0.596025076 0.233078418 0.853249111 -0.285822360
[41] 0.486532999 1.186218849 0.632651896 -1.340651425 0.869184491
[46] -0.773460454 -0.897107003 1.625212131 0.101241576 -1.037235396
[51] -0.572655474 0.007281009 0.426810552 -0.518495434 0.114265920
[56] 0.142004273 0.493977482 -1.451855794 -0.626590737 0.049274366
[61] -0.706817575 -0.592081893 -0.094835348 -0.043309897 -0.264362552
[66] 0.029344977 0.975351465 0.036456554 -1.310646102 0.984447037
[71] -0.570136804 0.049756911 0.608219313 -0.080807626 1.453718122
[76] -1.139939311 0.322247520 -2.200206836 1.157057735 -0.794121780
[81] -0.168259537 -0.521008531 -1.521857333 -2.027906964 -2.376345057
[86] 0.573422964 0.887490994 1.087546388 2.166787802 -1.829151667
[91] 0.867032669 -0.845752571 -0.421414788 -1.543350626 1.582259892
[96] -0.156058239 0.398309319 -0.460206501 1.158191391 1.330062993
> colVars(tmp)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> colSd(tmp)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> colMax(tmp)
[1] 0.702193186 -0.521402513 -0.775878314 0.222183990 -1.219836439
[6] 0.229487890 -1.344296329 -0.113096443 2.008796643 -0.952707912
[11] 2.152163492 0.716724724 -0.442323724 -0.121131820 1.934651509
[16] -0.585063822 -0.318226056 1.838997759 -0.123727871 0.224661361
[21] 0.539996312 0.148277850 0.196121471 -0.331367234 0.843580372
[26] -0.727632342 0.689264449 -0.263867790 0.517438408 -0.707217228
[31] -0.375451654 -1.437634975 0.978108581 -1.193986594 -1.454754954
[36] 1.367046007 -0.596025076 0.233078418 0.853249111 -0.285822360
[41] 0.486532999 1.186218849 0.632651896 -1.340651425 0.869184491
[46] -0.773460454 -0.897107003 1.625212131 0.101241576 -1.037235396
[51] -0.572655474 0.007281009 0.426810552 -0.518495434 0.114265920
[56] 0.142004273 0.493977482 -1.451855794 -0.626590737 0.049274366
[61] -0.706817575 -0.592081893 -0.094835348 -0.043309897 -0.264362552
[66] 0.029344977 0.975351465 0.036456554 -1.310646102 0.984447037
[71] -0.570136804 0.049756911 0.608219313 -0.080807626 1.453718122
[76] -1.139939311 0.322247520 -2.200206836 1.157057735 -0.794121780
[81] -0.168259537 -0.521008531 -1.521857333 -2.027906964 -2.376345057
[86] 0.573422964 0.887490994 1.087546388 2.166787802 -1.829151667
[91] 0.867032669 -0.845752571 -0.421414788 -1.543350626 1.582259892
[96] -0.156058239 0.398309319 -0.460206501 1.158191391 1.330062993
> colMin(tmp)
[1] 0.702193186 -0.521402513 -0.775878314 0.222183990 -1.219836439
[6] 0.229487890 -1.344296329 -0.113096443 2.008796643 -0.952707912
[11] 2.152163492 0.716724724 -0.442323724 -0.121131820 1.934651509
[16] -0.585063822 -0.318226056 1.838997759 -0.123727871 0.224661361
[21] 0.539996312 0.148277850 0.196121471 -0.331367234 0.843580372
[26] -0.727632342 0.689264449 -0.263867790 0.517438408 -0.707217228
[31] -0.375451654 -1.437634975 0.978108581 -1.193986594 -1.454754954
[36] 1.367046007 -0.596025076 0.233078418 0.853249111 -0.285822360
[41] 0.486532999 1.186218849 0.632651896 -1.340651425 0.869184491
[46] -0.773460454 -0.897107003 1.625212131 0.101241576 -1.037235396
[51] -0.572655474 0.007281009 0.426810552 -0.518495434 0.114265920
[56] 0.142004273 0.493977482 -1.451855794 -0.626590737 0.049274366
[61] -0.706817575 -0.592081893 -0.094835348 -0.043309897 -0.264362552
[66] 0.029344977 0.975351465 0.036456554 -1.310646102 0.984447037
[71] -0.570136804 0.049756911 0.608219313 -0.080807626 1.453718122
[76] -1.139939311 0.322247520 -2.200206836 1.157057735 -0.794121780
[81] -0.168259537 -0.521008531 -1.521857333 -2.027906964 -2.376345057
[86] 0.573422964 0.887490994 1.087546388 2.166787802 -1.829151667
[91] 0.867032669 -0.845752571 -0.421414788 -1.543350626 1.582259892
[96] -0.156058239 0.398309319 -0.460206501 1.158191391 1.330062993
> colMedians(tmp)
[1] 0.702193186 -0.521402513 -0.775878314 0.222183990 -1.219836439
[6] 0.229487890 -1.344296329 -0.113096443 2.008796643 -0.952707912
[11] 2.152163492 0.716724724 -0.442323724 -0.121131820 1.934651509
[16] -0.585063822 -0.318226056 1.838997759 -0.123727871 0.224661361
[21] 0.539996312 0.148277850 0.196121471 -0.331367234 0.843580372
[26] -0.727632342 0.689264449 -0.263867790 0.517438408 -0.707217228
[31] -0.375451654 -1.437634975 0.978108581 -1.193986594 -1.454754954
[36] 1.367046007 -0.596025076 0.233078418 0.853249111 -0.285822360
[41] 0.486532999 1.186218849 0.632651896 -1.340651425 0.869184491
[46] -0.773460454 -0.897107003 1.625212131 0.101241576 -1.037235396
[51] -0.572655474 0.007281009 0.426810552 -0.518495434 0.114265920
[56] 0.142004273 0.493977482 -1.451855794 -0.626590737 0.049274366
[61] -0.706817575 -0.592081893 -0.094835348 -0.043309897 -0.264362552
[66] 0.029344977 0.975351465 0.036456554 -1.310646102 0.984447037
[71] -0.570136804 0.049756911 0.608219313 -0.080807626 1.453718122
[76] -1.139939311 0.322247520 -2.200206836 1.157057735 -0.794121780
[81] -0.168259537 -0.521008531 -1.521857333 -2.027906964 -2.376345057
[86] 0.573422964 0.887490994 1.087546388 2.166787802 -1.829151667
[91] 0.867032669 -0.845752571 -0.421414788 -1.543350626 1.582259892
[96] -0.156058239 0.398309319 -0.460206501 1.158191391 1.330062993
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] 0.7021932 -0.5214025 -0.7758783 0.222184 -1.219836 0.2294879 -1.344296
[2,] 0.7021932 -0.5214025 -0.7758783 0.222184 -1.219836 0.2294879 -1.344296
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] -0.1130964 2.008797 -0.9527079 2.152163 0.7167247 -0.4423237 -0.1211318
[2,] -0.1130964 2.008797 -0.9527079 2.152163 0.7167247 -0.4423237 -0.1211318
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] 1.934652 -0.5850638 -0.3182261 1.838998 -0.1237279 0.2246614 0.5399963
[2,] 1.934652 -0.5850638 -0.3182261 1.838998 -0.1237279 0.2246614 0.5399963
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] 0.1482779 0.1961215 -0.3313672 0.8435804 -0.7276323 0.6892644 -0.2638678
[2,] 0.1482779 0.1961215 -0.3313672 0.8435804 -0.7276323 0.6892644 -0.2638678
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] 0.5174384 -0.7072172 -0.3754517 -1.437635 0.9781086 -1.193987 -1.454755
[2,] 0.5174384 -0.7072172 -0.3754517 -1.437635 0.9781086 -1.193987 -1.454755
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] 1.367046 -0.5960251 0.2330784 0.8532491 -0.2858224 0.486533 1.186219
[2,] 1.367046 -0.5960251 0.2330784 0.8532491 -0.2858224 0.486533 1.186219
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] 0.6326519 -1.340651 0.8691845 -0.7734605 -0.897107 1.625212 0.1012416
[2,] 0.6326519 -1.340651 0.8691845 -0.7734605 -0.897107 1.625212 0.1012416
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] -1.037235 -0.5726555 0.007281009 0.4268106 -0.5184954 0.1142659 0.1420043
[2,] -1.037235 -0.5726555 0.007281009 0.4268106 -0.5184954 0.1142659 0.1420043
[,57] [,58] [,59] [,60] [,61] [,62]
[1,] 0.4939775 -1.451856 -0.6265907 0.04927437 -0.7068176 -0.5920819
[2,] 0.4939775 -1.451856 -0.6265907 0.04927437 -0.7068176 -0.5920819
[,63] [,64] [,65] [,66] [,67] [,68]
[1,] -0.09483535 -0.0433099 -0.2643626 0.02934498 0.9753515 0.03645655
[2,] -0.09483535 -0.0433099 -0.2643626 0.02934498 0.9753515 0.03645655
[,69] [,70] [,71] [,72] [,73] [,74] [,75]
[1,] -1.310646 0.984447 -0.5701368 0.04975691 0.6082193 -0.08080763 1.453718
[2,] -1.310646 0.984447 -0.5701368 0.04975691 0.6082193 -0.08080763 1.453718
[,76] [,77] [,78] [,79] [,80] [,81] [,82]
[1,] -1.139939 0.3222475 -2.200207 1.157058 -0.7941218 -0.1682595 -0.5210085
[2,] -1.139939 0.3222475 -2.200207 1.157058 -0.7941218 -0.1682595 -0.5210085
[,83] [,84] [,85] [,86] [,87] [,88] [,89]
[1,] -1.521857 -2.027907 -2.376345 0.573423 0.887491 1.087546 2.166788
[2,] -1.521857 -2.027907 -2.376345 0.573423 0.887491 1.087546 2.166788
[,90] [,91] [,92] [,93] [,94] [,95] [,96]
[1,] -1.829152 0.8670327 -0.8457526 -0.4214148 -1.543351 1.58226 -0.1560582
[2,] -1.829152 0.8670327 -0.8457526 -0.4214148 -1.543351 1.58226 -0.1560582
[,97] [,98] [,99] [,100]
[1,] 0.3983093 -0.4602065 1.158191 1.330063
[2,] 0.3983093 -0.4602065 1.158191 1.330063
>
>
> Max(tmp2)
[1] 2.583377
> Min(tmp2)
[1] -2.640924
> mean(tmp2)
[1] -0.04141773
> Sum(tmp2)
[1] -4.141773
> Var(tmp2)
[1] 1.073796
>
> rowMeans(tmp2)
[1] 0.0005958177 -0.1783948892 -1.7727487076 2.5726073828 -0.8985844998
[6] -0.1852669868 0.6949295232 0.4666746279 -0.7341776529 -0.2339771375
[11] -0.2138370573 0.1099870902 1.1032624703 0.8486687892 -0.3065165491
[16] -1.6431485667 0.4006838366 1.4730513052 -0.2039456268 0.8539151274
[21] 0.8952102570 -0.6981547015 -0.1460583970 -0.2038131613 0.8466916002
[26] 0.5358976956 -0.2255228430 -0.7943601473 1.8554392742 0.5477212367
[31] -0.5660264701 0.3636086183 1.2199801245 -0.3860475939 0.1298271410
[36] -0.7457694478 -0.3196137582 -0.0504316774 0.4316881876 0.4792913741
[41] 1.3264192773 -1.7712501019 1.0191741874 -0.4110636075 -1.5700500068
[46] 0.2681906151 1.0802320113 -1.0861403763 -0.9891575032 1.3535303662
[51] 1.9161723764 -0.8986883847 -0.0147490080 1.5264764293 0.6109832638
[56] 0.3116303162 -0.0030286443 0.3689226441 -0.0482463520 0.1936610217
[61] -1.2404842156 -0.1970792848 -0.7511817242 -0.5676327008 0.5533689029
[66] 2.5833770476 -0.5824605690 0.0533873196 -0.7151681225 0.8959942690
[71] -0.3555167493 -2.6380424162 0.6581251740 -1.5080884744 -0.4356500801
[76] 0.5200274543 -1.2332112450 -2.1108058335 -0.7951473315 -0.8034956411
[81] 0.6284618513 -0.2502784127 0.0989575154 0.9825767115 -0.3206653064
[86] 1.6707090957 0.3580684384 -1.1514955308 -0.9537833066 0.6174041104
[91] 0.2127124150 -0.7597529199 -0.0734344955 -1.3259630188 0.6792289272
[96] -2.2646155720 -1.0560088863 1.8944019755 -2.6409240766 -0.3240427935
> rowSums(tmp2)
[1] 0.0005958177 -0.1783948892 -1.7727487076 2.5726073828 -0.8985844998
[6] -0.1852669868 0.6949295232 0.4666746279 -0.7341776529 -0.2339771375
[11] -0.2138370573 0.1099870902 1.1032624703 0.8486687892 -0.3065165491
[16] -1.6431485667 0.4006838366 1.4730513052 -0.2039456268 0.8539151274
[21] 0.8952102570 -0.6981547015 -0.1460583970 -0.2038131613 0.8466916002
[26] 0.5358976956 -0.2255228430 -0.7943601473 1.8554392742 0.5477212367
[31] -0.5660264701 0.3636086183 1.2199801245 -0.3860475939 0.1298271410
[36] -0.7457694478 -0.3196137582 -0.0504316774 0.4316881876 0.4792913741
[41] 1.3264192773 -1.7712501019 1.0191741874 -0.4110636075 -1.5700500068
[46] 0.2681906151 1.0802320113 -1.0861403763 -0.9891575032 1.3535303662
[51] 1.9161723764 -0.8986883847 -0.0147490080 1.5264764293 0.6109832638
[56] 0.3116303162 -0.0030286443 0.3689226441 -0.0482463520 0.1936610217
[61] -1.2404842156 -0.1970792848 -0.7511817242 -0.5676327008 0.5533689029
[66] 2.5833770476 -0.5824605690 0.0533873196 -0.7151681225 0.8959942690
[71] -0.3555167493 -2.6380424162 0.6581251740 -1.5080884744 -0.4356500801
[76] 0.5200274543 -1.2332112450 -2.1108058335 -0.7951473315 -0.8034956411
[81] 0.6284618513 -0.2502784127 0.0989575154 0.9825767115 -0.3206653064
[86] 1.6707090957 0.3580684384 -1.1514955308 -0.9537833066 0.6174041104
[91] 0.2127124150 -0.7597529199 -0.0734344955 -1.3259630188 0.6792289272
[96] -2.2646155720 -1.0560088863 1.8944019755 -2.6409240766 -0.3240427935
> rowVars(tmp2)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> rowSd(tmp2)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> rowMax(tmp2)
[1] 0.0005958177 -0.1783948892 -1.7727487076 2.5726073828 -0.8985844998
[6] -0.1852669868 0.6949295232 0.4666746279 -0.7341776529 -0.2339771375
[11] -0.2138370573 0.1099870902 1.1032624703 0.8486687892 -0.3065165491
[16] -1.6431485667 0.4006838366 1.4730513052 -0.2039456268 0.8539151274
[21] 0.8952102570 -0.6981547015 -0.1460583970 -0.2038131613 0.8466916002
[26] 0.5358976956 -0.2255228430 -0.7943601473 1.8554392742 0.5477212367
[31] -0.5660264701 0.3636086183 1.2199801245 -0.3860475939 0.1298271410
[36] -0.7457694478 -0.3196137582 -0.0504316774 0.4316881876 0.4792913741
[41] 1.3264192773 -1.7712501019 1.0191741874 -0.4110636075 -1.5700500068
[46] 0.2681906151 1.0802320113 -1.0861403763 -0.9891575032 1.3535303662
[51] 1.9161723764 -0.8986883847 -0.0147490080 1.5264764293 0.6109832638
[56] 0.3116303162 -0.0030286443 0.3689226441 -0.0482463520 0.1936610217
[61] -1.2404842156 -0.1970792848 -0.7511817242 -0.5676327008 0.5533689029
[66] 2.5833770476 -0.5824605690 0.0533873196 -0.7151681225 0.8959942690
[71] -0.3555167493 -2.6380424162 0.6581251740 -1.5080884744 -0.4356500801
[76] 0.5200274543 -1.2332112450 -2.1108058335 -0.7951473315 -0.8034956411
[81] 0.6284618513 -0.2502784127 0.0989575154 0.9825767115 -0.3206653064
[86] 1.6707090957 0.3580684384 -1.1514955308 -0.9537833066 0.6174041104
[91] 0.2127124150 -0.7597529199 -0.0734344955 -1.3259630188 0.6792289272
[96] -2.2646155720 -1.0560088863 1.8944019755 -2.6409240766 -0.3240427935
> rowMin(tmp2)
[1] 0.0005958177 -0.1783948892 -1.7727487076 2.5726073828 -0.8985844998
[6] -0.1852669868 0.6949295232 0.4666746279 -0.7341776529 -0.2339771375
[11] -0.2138370573 0.1099870902 1.1032624703 0.8486687892 -0.3065165491
[16] -1.6431485667 0.4006838366 1.4730513052 -0.2039456268 0.8539151274
[21] 0.8952102570 -0.6981547015 -0.1460583970 -0.2038131613 0.8466916002
[26] 0.5358976956 -0.2255228430 -0.7943601473 1.8554392742 0.5477212367
[31] -0.5660264701 0.3636086183 1.2199801245 -0.3860475939 0.1298271410
[36] -0.7457694478 -0.3196137582 -0.0504316774 0.4316881876 0.4792913741
[41] 1.3264192773 -1.7712501019 1.0191741874 -0.4110636075 -1.5700500068
[46] 0.2681906151 1.0802320113 -1.0861403763 -0.9891575032 1.3535303662
[51] 1.9161723764 -0.8986883847 -0.0147490080 1.5264764293 0.6109832638
[56] 0.3116303162 -0.0030286443 0.3689226441 -0.0482463520 0.1936610217
[61] -1.2404842156 -0.1970792848 -0.7511817242 -0.5676327008 0.5533689029
[66] 2.5833770476 -0.5824605690 0.0533873196 -0.7151681225 0.8959942690
[71] -0.3555167493 -2.6380424162 0.6581251740 -1.5080884744 -0.4356500801
[76] 0.5200274543 -1.2332112450 -2.1108058335 -0.7951473315 -0.8034956411
[81] 0.6284618513 -0.2502784127 0.0989575154 0.9825767115 -0.3206653064
[86] 1.6707090957 0.3580684384 -1.1514955308 -0.9537833066 0.6174041104
[91] 0.2127124150 -0.7597529199 -0.0734344955 -1.3259630188 0.6792289272
[96] -2.2646155720 -1.0560088863 1.8944019755 -2.6409240766 -0.3240427935
>
> colMeans(tmp2)
[1] -0.04141773
> colSums(tmp2)
[1] -4.141773
> colVars(tmp2)
[1] 1.073796
> colSd(tmp2)
[1] 1.036241
> colMax(tmp2)
[1] 2.583377
> colMin(tmp2)
[1] -2.640924
> colMedians(tmp2)
[1] -0.06193309
> colRanges(tmp2)
[,1]
[1,] -2.640924
[2,] 2.583377
>
> dataset1 <- matrix(dataset1,1,100)
>
> agree.checks(tmp,dataset1)
>
> dataset2 <- matrix(dataset2,100,1)
> agree.checks(tmp2,dataset2)
>
>
> tmp <- createBufferedMatrix(10,10)
>
> tmp[1:10,1:10] <- rnorm(100)
> colApply(tmp,sum)
[1] 2.4041170 5.5137706 -4.8475741 -1.5025128 -3.9121849 -2.2760350
[7] 4.5420144 0.4067960 -0.5780025 -0.5627931
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.64965026
[2,] -0.39044951
[3,] -0.02864551
[4,] 0.71161788
[5,] 2.42414337
>
> rowApply(tmp,sum)
[1] 1.1606537 0.3353231 5.0191743 -1.1651455 -3.1484385 0.6368650
[7] -1.5443228 0.1993119 -0.3562357 -1.9495897
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 7 9 10 2 1 3 7 5 8 7
[2,] 10 2 9 10 7 8 10 6 10 9
[3,] 5 5 5 7 4 9 1 9 3 1
[4,] 2 8 4 9 6 7 8 1 1 3
[5,] 3 7 1 4 5 6 5 3 5 2
[6,] 6 4 7 5 3 4 9 4 2 4
[7,] 8 1 3 3 10 10 6 7 9 10
[8,] 4 10 8 1 9 5 2 2 4 8
[9,] 9 3 6 8 2 2 3 8 6 6
[10,] 1 6 2 6 8 1 4 10 7 5
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] -0.29909582 1.24978475 -1.55367804 -0.08537035 0.12572905 -0.31444687
[7] 1.42188813 1.20762796 1.80692761 4.30660641 -2.02107039 0.55962829
[13] 2.32285598 2.67496299 0.29344872 -1.39000987 -5.49218230 -0.85982696
[19] -0.05745992 -3.59927362
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.44707389
[2,] -0.56461880
[3,] -0.06779305
[4,] 0.25491445
[5,] 1.52547547
>
> rowApply(tmp,sum)
[1] 1.81414319 4.50579385 0.63428410 -6.73885370 0.08167832
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 6 19 10 5 10
[2,] 15 11 2 11 17
[3,] 12 2 9 6 18
[4,] 18 4 12 7 6
[5,] 10 8 8 14 14
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] -0.56461880 0.584601789 -0.001403865 1.5837818 -0.14161746 1.3020956
[2,] 1.52547547 0.374891604 -1.077298644 -0.6237435 -0.02104759 0.5611862
[3,] -0.06779305 -0.945945378 -0.420168816 0.1768797 -0.56243353 -0.6645191
[4,] -1.44707389 -0.004171475 -1.303096518 -0.9968807 0.29617187 0.4290787
[5,] 0.25491445 1.240408214 1.248289804 -0.2254076 0.55465576 -1.9422883
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] -0.4815568 -0.1275911 -1.4243278 2.9767847 -0.4498972 -1.3997966
[2,] 0.2602438 1.0320625 1.7318907 1.1778612 0.7909763 0.4877441
[3,] 0.1080350 -0.8834520 0.2089759 -0.6473853 -0.6588161 0.4936099
[4,] 0.8322084 0.7229996 0.8653611 -0.4532947 0.2288196 1.0857729
[5,] 0.7029577 0.4636089 0.4250277 1.2526406 -1.9321530 -0.1077020
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] 1.2777901 1.9938507 0.3901952 -0.8874497 -0.3214463 -1.57451080
[2,] -0.6005978 -0.6053674 0.1816262 -0.9981907 -1.2124038 0.48353744
[3,] 2.7453094 1.2053525 0.8540780 0.4354406 -0.8101149 0.37835333
[4,] 0.4640702 -0.5202976 -1.5337426 -1.8019816 -2.0334916 -0.07681371
[5,] -1.5637160 0.6014248 0.4012919 1.8621715 -1.1147258 -0.07039323
[,19] [,20]
[1,] -1.0183631 0.09762272
[2,] 1.4372277 -0.40027988
[3,] 1.4797357 -1.79085803
[4,] 0.1448329 -1.63732472
[5,] -2.1008931 0.13156629
>
>
> is.BufferedMatrix(tmp)
[1] TRUE
>
> as.BufferedMatrix(as.matrix(tmp))
BufferedMatrix object
Matrix size: 5 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 800 bytes.
>
>
>
> subBufferedMatrix(tmp,1:5,1:5)
BufferedMatrix object
Matrix size: 5 5
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 655 bytes.
Disk usage : 200 bytes.
> subBufferedMatrix(tmp,,5:8)
BufferedMatrix object
Matrix size: 5 4
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 567 bytes.
Disk usage : 160 bytes.
> subBufferedMatrix(tmp,1:3,)
BufferedMatrix object
Matrix size: 3 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 480 bytes.
>
>
> rm(tmp)
>
>
> ###
> ### Testing colnames and rownames
> ###
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
>
>
> colnames(tmp)
NULL
> rownames(tmp)
NULL
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> colnames(tmp)
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
> rownames(tmp)
[1] "row1" "row2" "row3" "row4" "row5"
>
>
> tmp["row1",]
col1 col2 col3 col4 col5 col6 col7
row1 0.4798539 -1.861981 1.104107 -0.2949884 0.7987685 0.6581588 -1.177619
col8 col9 col10 col11 col12 col13 col14
row1 -0.1709075 -1.27908 1.528961 -2.110521 -0.2893533 0.5419736 0.7425861
col15 col16 col17 col18 col19 col20
row1 -0.7816014 0.00408043 -1.233475 -2.07947 0.7785126 -0.6848915
> tmp[,"col10"]
col10
row1 1.5289614
row2 -1.4829279
row3 1.1076216
row4 -0.7574108
row5 0.8436722
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7
row1 0.4798539 -1.8619810 1.104107 -0.2949884 0.7987685 0.6581588 -1.1776193
row5 0.3449228 0.4636855 -1.713430 -0.8609984 0.3435009 1.3695878 -0.8348955
col8 col9 col10 col11 col12 col13
row1 -0.1709075 -1.2790803 1.5289614 -2.110521 -0.2893533 0.5419736
row5 1.2683308 -0.5972268 0.8436722 1.336677 0.2958410 -0.9416810
col14 col15 col16 col17 col18 col19
row1 0.74258608 -0.7816014 0.00408043 -1.233475 -2.0794698 0.7785126
row5 -0.06325642 0.4614977 -0.66659698 -1.192814 0.9984015 -0.7591346
col20
row1 -0.6848915
row5 -1.6322757
> tmp[,c("col6","col20")]
col6 col20
row1 0.6581588 -0.6848915
row2 0.2657643 0.2714601
row3 2.0623742 -0.4795124
row4 -2.3349575 0.4049219
row5 1.3695878 -1.6322757
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 0.6581588 -0.6848915
row5 1.3695878 -1.6322757
>
>
>
>
> tmp["row1",] <- rnorm(20,mean=10)
> tmp[,"col10"] <- rnorm(5,mean=30)
> tmp[c("row1","row5"),] <- rnorm(40,mean=50)
> tmp[,c("col6","col20")] <- rnorm(10,mean=75)
> tmp[c("row1","row5"),c("col6","col20")] <- rnorm(4,mean=105)
>
> tmp["row1",]
col1 col2 col3 col4 col5 col6 col7 col8
row1 49.79013 48.98117 51.09912 48.77761 49.85957 104.6341 49.34799 49.51745
col9 col10 col11 col12 col13 col14 col15 col16
row1 50.02523 48.81454 50.27519 48.89987 49.62617 49.06874 49.48358 50.59132
col17 col18 col19 col20
row1 49.01921 49.8649 50.57816 104.0782
> tmp[,"col10"]
col10
row1 48.81454
row2 30.82619
row3 28.30322
row4 30.25668
row5 50.46341
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 49.79013 48.98117 51.09912 48.77761 49.85957 104.6341 49.34799 49.51745
row5 48.68293 50.20048 51.23600 52.02482 49.40962 105.2748 48.86859 48.70196
col9 col10 col11 col12 col13 col14 col15 col16
row1 50.02523 48.81454 50.27519 48.89987 49.62617 49.06874 49.48358 50.59132
row5 49.35687 50.46341 49.35939 49.91386 48.89174 48.52070 49.85918 50.50166
col17 col18 col19 col20
row1 49.01921 49.86490 50.57816 104.0782
row5 50.80798 49.65872 50.13415 105.8860
> tmp[,c("col6","col20")]
col6 col20
row1 104.63414 104.07824
row2 75.91864 75.12492
row3 74.74361 76.34525
row4 74.17345 74.91838
row5 105.27478 105.88596
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 104.6341 104.0782
row5 105.2748 105.8860
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 104.6341 104.0782
row5 105.2748 105.8860
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] -0.2188867
[2,] 0.9069305
[3,] 0.4643199
[4,] -0.4166714
[5,] -0.2260295
> tmp[,c("col17","col7")]
col17 col7
[1,] 0.5754140 1.70211380
[2,] 0.4905868 -1.74306553
[3,] 0.1149879 -0.05959012
[4,] -0.8563055 -0.18088579
[5,] -1.6524316 0.66085720
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] -0.54304278 0.8180482
[2,] -0.09204923 -0.9593275
[3,] -0.99286318 0.5421834
[4,] 0.71692876 -1.4247501
[5,] -1.50633836 -2.8129067
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] -0.5430428
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] -0.54304278
[2,] -0.09204923
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
>
>
>
> subBufferedMatrix(tmp,c("row3","row1"),)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6]
row3 -0.6689243 1.0039545 2.2161044 -0.0003085884 0.4176729 -0.3958038
row1 1.2956071 0.2717957 -0.2035364 -1.9867267159 0.0682616 -1.7140306
[,7] [,8] [,9] [,10] [,11] [,12]
row3 -0.3649508 -0.3837806 0.5852097 -1.8125702 0.4523783 0.1420507
row1 0.4695393 1.1072962 -0.4156020 -0.4177497 -0.2180680 0.3176841
[,13] [,14] [,15] [,16] [,17] [,18]
row3 -1.1696765 -0.3316184 0.2613119 1.4683451 0.2554522 -0.6353408
row1 0.7354161 -0.1281373 -0.1669947 0.4046768 -0.7032211 0.9463710
[,19] [,20]
row3 -2.1153964 1.442197
row1 0.9370413 0.344929
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 -1.439327 0.814827 -0.09508605 -0.8434713 0.7283394 -0.7059927 0.7170654
[,8] [,9] [,10]
row2 0.1933449 -0.7205954 0.4469513
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 0.334676 -2.419111 2.687235 0.7032046 -0.109436 0.1477899 2.501075
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 1.490177 0.5728236 0.2821036 0.4772756 1.483873 0.6431976 0.7506901
[,15] [,16] [,17] [,18] [,19] [,20]
row5 1.537405 0.5899014 1.101532 -1.55327 -0.5145225 0.940872
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> colnames(tmp)
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
> rownames(tmp)
[1] "row1" "row2" "row3" "row4" "row5"
>
>
> colnames(tmp) <- NULL
> rownames(tmp) <- NULL
>
> colnames(tmp)
NULL
> rownames(tmp)
NULL
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> dimnames(tmp)
[[1]]
[1] "row1" "row2" "row3" "row4" "row5"
[[2]]
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
>
> dimnames(tmp) <- NULL
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> dimnames(tmp)
[[1]]
NULL
[[2]]
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
>
>
> dimnames(tmp) <- NULL
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
> dimnames(tmp)
[[1]]
[1] "row1" "row2" "row3" "row4" "row5"
[[2]]
NULL
>
> dimnames(tmp) <- list(NULL,c(colnames(tmp,do.NULL=FALSE)))
> dimnames(tmp)
[[1]]
NULL
[[2]]
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
>
>
>
> ###
> ### Testing logical indexing
> ###
> ###
>
> tmp <- createBufferedMatrix(230,15)
> tmp[1:230,1:15] <- rnorm(230*15)
> x <-tmp[1:230,1:15]
>
> for (rep in 1:10){
+ which.cols <- sample(c(TRUE,FALSE),15,replace=T)
+ which.rows <- sample(c(TRUE,FALSE),230,replace=T)
+
+ if (!all(tmp[which.rows,which.cols] == x[which.rows,which.cols])){
+ stop("No agreement when logical indexing\n")
+ }
+
+ if (!all(subBufferedMatrix(tmp,,which.cols)[,1:sum(which.cols)] == x[,which.cols])){
+ stop("No agreement when logical indexing in subBufferedMatrix cols\n")
+ }
+ if (!all(subBufferedMatrix(tmp,which.rows,)[1:sum(which.rows),] == x[which.rows,])){
+ stop("No agreement when logical indexing in subBufferedMatrix rows\n")
+ }
+
+
+ if (!all(subBufferedMatrix(tmp,which.rows,which.cols)[1:sum(which.rows),1:sum(which.cols)]== x[which.rows,which.cols])){
+ stop("No agreement when logical indexing in subBufferedMatrix rows and columns\n")
+ }
+ }
>
>
> ##
> ## Test the ReadOnlyMode
> ##
>
> ReadOnlyMode(tmp)
<pointer: 0x600003f7c060>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM1302f36329132"
[2] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM1302f31da856a"
[3] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM1302f16d0bb8"
[4] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM1302f1e1c5dc3"
[5] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM1302f584fbca6"
[6] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM1302f5aea6395"
[7] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM1302f522ff9d4"
[8] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM1302f4bbaf773"
[9] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM1302f5fcbc5dc"
[10] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM1302f3b2b1fa6"
[11] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM1302fc2ae9a3"
[12] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM1302f5550d292"
[13] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM1302f2d309b00"
[14] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM1302f5210342d"
[15] "/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM1302f25d1a072"
>
>
> ### testing coercion functions
> ###
>
> tmp <- as(tmp,"matrix")
> tmp <- as(tmp,"BufferedMatrix")
>
>
>
> ### testing whether can move storage from one location to another
>
> MoveStorageDirectory(tmp,"NewDirectory",full.path=FALSE)
<pointer: 0x600003f64120>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x600003f64120>
Warning message:
In dir.create(new.directory) :
'/Users/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x600003f64120>
> rowMedians(tmp)
[1] 1.893240e-01 2.866342e-01 -2.142198e-01 -2.747214e-02 -1.658451e-01
[6] -3.865325e-02 -1.127909e-01 1.869250e-01 -1.225709e-01 4.495973e-01
[11] -1.367074e-02 -1.684961e-01 6.363953e-05 -1.962311e-01 7.757554e-01
[16] 3.084038e-01 1.377974e-01 2.502040e-02 1.209914e-01 2.589894e-01
[21] -3.045594e-01 -1.084290e-02 2.029676e-01 -2.608903e-01 1.066794e-01
[26] 1.186554e-01 -1.503665e-01 3.056944e-01 8.524216e-02 -2.124444e-01
[31] -1.987144e-01 1.184355e-01 -8.185969e-01 -3.933075e-02 -6.702439e-01
[36] -6.188559e-02 4.056276e-02 -4.978758e-01 -1.134676e-01 5.847423e-01
[41] -4.160455e-01 1.244799e-01 -4.535889e-01 -1.922778e-01 -2.039095e-01
[46] 8.114143e-02 3.870103e-01 3.564893e-02 -3.578244e-01 1.577858e-01
[51] -4.345644e-01 -1.165453e-01 4.843419e-01 -2.637243e-01 -2.932953e-02
[56] 4.766403e-01 -1.766861e-01 -2.171164e-01 -4.159689e-01 5.494499e-02
[61] 9.605063e-03 6.883925e-01 5.197147e-01 1.025101e-01 -2.765217e-01
[66] 4.968262e-01 1.493742e-01 -6.281512e-01 -4.813393e-02 -3.943242e-01
[71] -4.857329e-01 -3.095269e-01 3.597039e-01 3.462654e-02 -1.394227e-01
[76] 1.568093e-02 1.553615e-01 2.808511e-01 -1.718027e-01 6.383259e-01
[81] -3.813510e-01 -4.087288e-01 1.315149e-01 -2.454087e-01 -5.171686e-02
[86] 4.795008e-02 7.289056e-02 -2.411597e-01 1.173524e-01 -1.605993e-01
[91] 3.071062e-01 -2.444526e-01 1.444891e-01 3.167182e-01 1.370239e-03
[96] -1.531590e-01 -2.581495e-01 -2.778736e-02 2.216862e-01 1.101064e-01
[101] -1.127733e-01 1.333522e-01 1.975375e-01 5.424761e-01 -7.183572e-02
[106] 2.024524e-01 2.970502e-01 -7.947750e-02 -1.658824e-01 3.426550e-01
[111] 3.707075e-02 -2.176807e-01 2.046020e-01 3.741167e-01 -3.351972e-01
[116] -7.765441e-02 -2.052049e-01 -2.005257e-01 6.027649e-01 2.651288e-01
[121] 5.085352e-01 3.564536e-01 5.356795e-01 1.888011e-02 1.422479e-01
[126] 7.862511e-01 1.106362e-01 -2.470132e-02 -5.280404e-01 1.432971e-03
[131] 8.113518e-02 -4.548721e-01 1.476271e-01 -1.699866e-01 5.978304e-02
[136] -1.419458e-01 3.471517e-01 2.496124e-01 1.314644e-01 4.315054e-01
[141] -2.487883e-01 2.679460e-01 -3.573855e-01 4.704805e-01 3.214645e-01
[146] 7.169322e-02 2.511081e-01 -3.466562e-01 8.977845e-02 -1.549094e-01
[151] -2.014701e-01 3.548878e-02 -2.105005e-01 -1.586404e-01 1.259167e-01
[156] 9.241055e-02 3.163420e-01 -2.035438e-02 -3.035511e-01 -1.263446e-01
[161] 1.412374e-01 -1.054976e-01 -2.983471e-01 6.303885e-02 2.605327e-01
[166] 9.932782e-02 2.700924e-01 1.897924e-01 -1.039422e-01 -5.507745e-02
[171] 1.317646e-01 1.221254e-01 2.798614e-01 -6.112604e-02 1.583043e-01
[176] -1.932241e-01 -2.753957e-01 2.141949e-01 4.234395e-01 2.914723e-01
[181] -1.232179e-01 1.438738e-01 -4.609053e-03 -1.760592e-01 -1.993533e-01
[186] -1.918459e-01 7.521865e-03 2.870189e-01 -7.577779e-02 4.408777e-01
[191] -5.228422e-01 -9.625957e-02 5.431296e-01 3.594238e-01 -1.214177e-02
[196] -5.644397e-02 -3.170897e-01 3.068890e-01 -2.217946e-01 2.654352e-01
[201] -4.990512e-02 -1.972250e-01 1.711689e-01 3.286597e-01 1.844567e-01
[206] 5.242545e-01 -4.191620e-01 -5.356749e-01 3.308390e-01 1.599829e-01
[211] 1.053145e+00 6.321779e-01 -4.475101e-01 -1.227487e-01 -1.526663e-01
[216] 1.748648e-01 8.780269e-02 6.585544e-02 1.246557e-01 5.049555e-01
[221] 1.764534e-02 -3.593459e-01 -3.125592e-01 2.397291e-02 2.964059e-01
[226] 3.567492e-01 -3.109614e-01 -5.019357e-02 3.573899e-02 5.301111e-01
>
> proc.time()
user system elapsed
2.720 15.337 18.555
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
> prefix <- "dbmtest"
> directory <- getwd()
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_Test_C",P)
RBufferedMatrix
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x600003f3c0c0>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x600003f3c0c0>
> .Call("R_bm_Test_C",P)
RBufferedMatrix
Checking dimensions
Rows: 5
Cols: 10
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x600003f3c0c0>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 10
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 1.000000 2.000000 3.000000 4.000000 0.000000 0.000000 0.000000 0.000000 0.000000
1.000000 2.000000 3.000000 4.000000 5.000000 0.000000 0.000000 0.000000 0.000000 0.000000
2.000000 3.000000 4.000000 5.000000 6.000000 0.000000 0.000000 0.000000 0.000000 0.000000
3.000000 4.000000 5.000000 6.000000 7.000000 0.000000 0.000000 0.000000 0.000000 0.000000
4.000000 5.000000 6.000000 7.000000 8.000000 0.000000 0.000000 0.000000 0.000000 0.000000
<pointer: 0x600003f3c0c0>
> rm(P)
>
> #P <- .Call("R_bm_Destroy",P)
> #.Call("R_bm_Destroy",P)
> #.Call("R_bm_Test_C",P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,5)
[1] TRUE
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 0
Buffer Rows: 1
Buffer Cols: 1
Printing Values
<pointer: 0x600003f60120>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003f60120>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 1
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000
0.000000
0.000000
0.000000
0.000000
<pointer: 0x600003f60120>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003f60120>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x600003f60120>
> rm(P)
>
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,5)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003f2c000>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003f2c000>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x600003f2c000>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x600003f2c000>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 5
Buffer Cols: 5
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x600003f2c000>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x600003f2c000>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 5
Buffer Cols: 5
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x600003f2c000>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x600003f2c000>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 5
Buffer Cols: 5
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x600003f2c000>
> rm(P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003f2c180>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x600003f2c180>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003f2c180>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003f2c180>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile13a825196940b" "BufferedMatrixFile13a8274d18805"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile13a825196940b" "BufferedMatrixFile13a8274d18805"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003f2c420>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003f2c420>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x600003f2c420>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x600003f2c420>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x600003f2c420>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x600003f2c420>
> .Call("R_bm_isRowMode",P)
[1] FALSE
> rm(P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003f2c600>
> .Call("R_bm_AddColumn",P)
<pointer: 0x600003f2c600>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x600003f2c600>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x600003f2c600>
> rm(P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_Test_C",P)
RBufferedMatrix
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x600003f28000>
> .Call("R_bm_getValue",P,3,3)
[1] 6
>
> .Call("R_bm_getValue",P,100000,10000)
[1] NA
> .Call("R_bm_setValue",P,3,3,12345.0)
[1] TRUE
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 12345.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x600003f28000>
> rm(P)
>
> proc.time()
user system elapsed
0.342 0.161 0.519
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
> Temp <- createBufferedMatrix(100)
> dim(Temp)
[1] 100 0
> buffer.dim(Temp)
[1] 1 1
>
>
> proc.time()
user system elapsed
0.327 0.103 0.443