Ben Bolstad
| Snapshot Date: 2026-03-20 13:40 -0400 (Fri, 20 Mar 2026) |
| 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 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-03-21 11:34 -0400 (Sat, 21 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences" | 4866 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-20 r89666) -- "Unsuffered Consequences" | 4545 |
| 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 257/2368 | 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 | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | ERROR | |||||||||
| See other builds for BufferedMatrix in R Universe. | ||||||||||||||
|
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: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BufferedMatrix_1.75.0.tar.gz |
| StartedAt: 2026-03-20 21:43:42 -0400 (Fri, 20 Mar 2026) |
| EndedAt: 2026-03-20 21:44:07 -0400 (Fri, 20 Mar 2026) |
| EllapsedTime: 25.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 0 |
##############################################################################
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### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BufferedMatrix_1.75.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck’
* using R Under development (unstable) (2026-03-05 r89546)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-03-21 01:43:42 UTC
* 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 ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* 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 loading without being on the library search path ... 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’ ...* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/00check.log’
for details.
BufferedMatrix.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL BufferedMatrix
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘BufferedMatrix’ ...
** this is package ‘BufferedMatrix’ version ‘1.75.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RBufferedMatrix.c -o RBufferedMatrix.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c doubleBufferedMatrix.c -o doubleBufferedMatrix.o
doubleBufferedMatrix.c: In function ‘dbm_ReadOnlyMode’:
doubleBufferedMatrix.c:1580:7: warning: suggest parentheses around operand of ‘!’ or change ‘&’ to ‘&&’ or ‘!’ to ‘~’ [-Wparentheses]
1580 | if (!(Matrix->readonly) & setting){
| ^~~~~~~~~~~~~~~~~~~
doubleBufferedMatrix.c: At top level:
doubleBufferedMatrix.c:3327:12: warning: ‘sort_double’ defined but not used [-Wunused-function]
3327 | static int sort_double(const double *a1,const double *a2){
| ^~~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c doubleBufferedMatrix_C_tests.c -o doubleBufferedMatrix_C_tests.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c init_package.c -o init_package.o
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o BufferedMatrix.so RBufferedMatrix.o doubleBufferedMatrix.o doubleBufferedMatrix_C_tests.o init_package.o -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-bioc/R/site-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) (2026-03-05 r89546) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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
0.250 0.039 0.276
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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] "/home/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) max used (Mb)
Ncells 479482 25.7 1050322 56.1 639251 34.2
Vcells 886403 6.8 8388608 64.0 2083267 15.9
>
>
>
>
> ##
> ## 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] "Fri Mar 20 21:43:57 2026"
> 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] "Fri Mar 20 21:43:57 2026"
>
>
> 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: 0x61c201d6b4f0>
>
>
>
> 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] "Fri Mar 20 21:43:58 2026"
> 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] "Fri Mar 20 21:43:58 2026"
>
> ColMode(tmp2)
<pointer: 0x61c201d6b4f0>
>
>
>
> ### 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,] 99.9539981 0.13989898 -0.005437868 2.6466910
[2,] -1.3788199 -1.68561578 1.700909370 -0.8830574
[3,] -1.2838938 0.87377069 -1.918140669 1.1827488
[4,] 0.1595672 0.07774388 0.886352477 -0.4460885
> ewApply(tmp5,abs)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/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,] 99.9539981 0.13989898 0.005437868 2.6466910
[2,] 1.3788199 1.68561578 1.700909370 0.8830574
[3,] 1.2838938 0.87377069 1.918140669 1.1827488
[4,] 0.1595672 0.07774388 0.886352477 0.4460885
> ewApply(tmp5,sqrt)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/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,] 9.9976996 0.3740307 0.0737419 1.6268654
[2,] 1.1742316 1.2983127 1.3041892 0.9397113
[3,] 1.1330904 0.9347570 1.3849696 1.0875425
[4,] 0.3994587 0.2788259 0.9414629 0.6678986
>
> 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: /home/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,] 224.93099 28.88021 25.74286 43.91534
[2,] 38.12114 39.66874 39.74280 35.28017
[3,] 37.61480 35.22134 40.76784 37.05817
[4,] 29.15415 27.86600 35.30098 32.12507
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x61c2033c95a0>
> exp(tmp5)
<pointer: 0x61c2033c95a0>
> log(tmp5,2)
<pointer: 0x61c2033c95a0>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 468.1644
> Min(tmp5)
[1] 53.50802
> mean(tmp5)
[1] 73.61262
> Sum(tmp5)
[1] 14722.52
> Var(tmp5)
[1] 860.1068
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 90.42605 70.72811 75.64393 72.14397 72.79537 71.44838 71.72045 70.50925
[9] 70.23761 70.47306
> rowSums(tmp5)
[1] 1808.521 1414.562 1512.879 1442.879 1455.907 1428.968 1434.409 1410.185
[9] 1404.752 1409.461
> rowVars(tmp5)
[1] 7998.30103 66.72496 66.73467 84.43297 101.02864 89.33855
[7] 47.23462 74.98678 57.65705 67.19976
> rowSd(tmp5)
[1] 89.433221 8.168535 8.169129 9.188742 10.051300 9.451907 6.872745
[8] 8.659491 7.593224 8.197546
> rowMax(tmp5)
[1] 468.16439 82.71943 97.93345 96.83644 94.56559 93.52824 88.77515
[8] 91.16910 86.52228 86.77020
> rowMin(tmp5)
[1] 53.58038 56.65447 61.54621 57.96465 53.50802 57.24452 60.24188 58.70952
[9] 59.07563 54.02380
>
> colMeans(tmp5)
[1] 106.98577 69.59144 71.71490 72.95534 72.42414 70.09328 73.75089
[8] 73.04364 75.57152 76.34176 67.89736 70.05995 67.76334 70.59076
[15] 74.37990 68.96458 71.74515 73.11953 70.83312 74.42603
> colSums(tmp5)
[1] 1069.8577 695.9144 717.1490 729.5534 724.2414 700.9328 737.5089
[8] 730.4364 755.7152 763.4176 678.9736 700.5995 677.6334 705.9076
[15] 743.7990 689.6458 717.4515 731.1953 708.3312 744.2603
> colVars(tmp5)
[1] 16168.80695 80.38184 95.35717 86.73385 34.92095 36.84599
[7] 129.25370 40.87397 43.09551 60.12769 102.40473 47.68575
[13] 123.82287 76.43726 131.97056 40.56526 23.93205 81.62456
[19] 66.35285 121.90234
> colSd(tmp5)
[1] 127.156624 8.965592 9.765100 9.313101 5.909395 6.070090
[7] 11.368980 6.393276 6.564717 7.754205 10.119522 6.905487
[13] 11.127572 8.742840 11.487844 6.369086 4.892039 9.034631
[19] 8.145726 11.040939
> colMax(tmp5)
[1] 468.16439 82.56529 84.85291 91.40404 80.26923 82.50485 96.83644
[8] 82.12199 86.25303 86.74339 82.28724 82.90519 93.52824 88.77515
[15] 94.56559 81.48424 77.61292 88.61258 78.45708 97.93345
> colMin(tmp5)
[1] 55.03385 57.99943 53.58038 61.93961 59.35391 58.70952 56.65447 63.85898
[9] 66.55164 64.91228 53.50802 59.07563 59.51264 57.96465 60.63030 58.93191
[17] 65.30085 54.28587 57.95342 57.24452
>
>
> ### 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] NA 70.72811 75.64393 72.14397 72.79537 71.44838 71.72045 70.50925
[9] 70.23761 70.47306
> rowSums(tmp5)
[1] NA 1414.562 1512.879 1442.879 1455.907 1428.968 1434.409 1410.185
[9] 1404.752 1409.461
> rowVars(tmp5)
[1] 8442.59515 66.72496 66.73467 84.43297 101.02864 89.33855
[7] 47.23462 74.98678 57.65705 67.19976
> rowSd(tmp5)
[1] 91.883596 8.168535 8.169129 9.188742 10.051300 9.451907 6.872745
[8] 8.659491 7.593224 8.197546
> rowMax(tmp5)
[1] NA 82.71943 97.93345 96.83644 94.56559 93.52824 88.77515 91.16910
[9] 86.52228 86.77020
> rowMin(tmp5)
[1] NA 56.65447 61.54621 57.96465 53.50802 57.24452 60.24188 58.70952
[9] 59.07563 54.02380
>
> colMeans(tmp5)
[1] 106.98577 69.59144 71.71490 NA 72.42414 70.09328 73.75089
[8] 73.04364 75.57152 76.34176 67.89736 70.05995 67.76334 70.59076
[15] 74.37990 68.96458 71.74515 73.11953 70.83312 74.42603
> colSums(tmp5)
[1] 1069.8577 695.9144 717.1490 NA 724.2414 700.9328 737.5089
[8] 730.4364 755.7152 763.4176 678.9736 700.5995 677.6334 705.9076
[15] 743.7990 689.6458 717.4515 731.1953 708.3312 744.2603
> colVars(tmp5)
[1] 16168.80695 80.38184 95.35717 NA 34.92095 36.84599
[7] 129.25370 40.87397 43.09551 60.12769 102.40473 47.68575
[13] 123.82287 76.43726 131.97056 40.56526 23.93205 81.62456
[19] 66.35285 121.90234
> colSd(tmp5)
[1] 127.156624 8.965592 9.765100 NA 5.909395 6.070090
[7] 11.368980 6.393276 6.564717 7.754205 10.119522 6.905487
[13] 11.127572 8.742840 11.487844 6.369086 4.892039 9.034631
[19] 8.145726 11.040939
> colMax(tmp5)
[1] 468.16439 82.56529 84.85291 NA 80.26923 82.50485 96.83644
[8] 82.12199 86.25303 86.74339 82.28724 82.90519 93.52824 88.77515
[15] 94.56559 81.48424 77.61292 88.61258 78.45708 97.93345
> colMin(tmp5)
[1] 55.03385 57.99943 53.58038 NA 59.35391 58.70952 56.65447 63.85898
[9] 66.55164 64.91228 53.50802 59.07563 59.51264 57.96465 60.63030 58.93191
[17] 65.30085 54.28587 57.95342 57.24452
>
> Max(tmp5,na.rm=TRUE)
[1] 468.1644
> Min(tmp5,na.rm=TRUE)
[1] 53.50802
> mean(tmp5,na.rm=TRUE)
[1] 73.52322
> Sum(tmp5,na.rm=TRUE)
[1] 14631.12
> Var(tmp5,na.rm=TRUE)
[1] 862.8441
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 90.37458 70.72811 75.64393 72.14397 72.79537 71.44838 71.72045 70.50925
[9] 70.23761 70.47306
> rowSums(tmp5,na.rm=TRUE)
[1] 1717.117 1414.562 1512.879 1442.879 1455.907 1428.968 1434.409 1410.185
[9] 1404.752 1409.461
> rowVars(tmp5,na.rm=TRUE)
[1] 8442.59515 66.72496 66.73467 84.43297 101.02864 89.33855
[7] 47.23462 74.98678 57.65705 67.19976
> rowSd(tmp5,na.rm=TRUE)
[1] 91.883596 8.168535 8.169129 9.188742 10.051300 9.451907 6.872745
[8] 8.659491 7.593224 8.197546
> rowMax(tmp5,na.rm=TRUE)
[1] 468.16439 82.71943 97.93345 96.83644 94.56559 93.52824 88.77515
[8] 91.16910 86.52228 86.77020
> rowMin(tmp5,na.rm=TRUE)
[1] 53.58038 56.65447 61.54621 57.96465 53.50802 57.24452 60.24188 58.70952
[9] 59.07563 54.02380
>
> colMeans(tmp5,na.rm=TRUE)
[1] 106.98577 69.59144 71.71490 70.90548 72.42414 70.09328 73.75089
[8] 73.04364 75.57152 76.34176 67.89736 70.05995 67.76334 70.59076
[15] 74.37990 68.96458 71.74515 73.11953 70.83312 74.42603
> colSums(tmp5,na.rm=TRUE)
[1] 1069.8577 695.9144 717.1490 638.1493 724.2414 700.9328 737.5089
[8] 730.4364 755.7152 763.4176 678.9736 700.5995 677.6334 705.9076
[15] 743.7990 689.6458 717.4515 731.1953 708.3312 744.2603
> colVars(tmp5,na.rm=TRUE)
[1] 16168.80695 80.38184 95.35717 50.30412 34.92095 36.84599
[7] 129.25370 40.87397 43.09551 60.12769 102.40473 47.68575
[13] 123.82287 76.43726 131.97056 40.56526 23.93205 81.62456
[19] 66.35285 121.90234
> colSd(tmp5,na.rm=TRUE)
[1] 127.156624 8.965592 9.765100 7.092540 5.909395 6.070090
[7] 11.368980 6.393276 6.564717 7.754205 10.119522 6.905487
[13] 11.127572 8.742840 11.487844 6.369086 4.892039 9.034631
[19] 8.145726 11.040939
> colMax(tmp5,na.rm=TRUE)
[1] 468.16439 82.56529 84.85291 82.45845 80.26923 82.50485 96.83644
[8] 82.12199 86.25303 86.74339 82.28724 82.90519 93.52824 88.77515
[15] 94.56559 81.48424 77.61292 88.61258 78.45708 97.93345
> colMin(tmp5,na.rm=TRUE)
[1] 55.03385 57.99943 53.58038 61.93961 59.35391 58.70952 56.65447 63.85898
[9] 66.55164 64.91228 53.50802 59.07563 59.51264 57.96465 60.63030 58.93191
[17] 65.30085 54.28587 57.95342 57.24452
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] NaN 70.72811 75.64393 72.14397 72.79537 71.44838 71.72045 70.50925
[9] 70.23761 70.47306
> rowSums(tmp5,na.rm=TRUE)
[1] 0.000 1414.562 1512.879 1442.879 1455.907 1428.968 1434.409 1410.185
[9] 1404.752 1409.461
> rowVars(tmp5,na.rm=TRUE)
[1] NA 66.72496 66.73467 84.43297 101.02864 89.33855 47.23462
[8] 74.98678 57.65705 67.19976
> rowSd(tmp5,na.rm=TRUE)
[1] NA 8.168535 8.169129 9.188742 10.051300 9.451907 6.872745
[8] 8.659491 7.593224 8.197546
> rowMax(tmp5,na.rm=TRUE)
[1] NA 82.71943 97.93345 96.83644 94.56559 93.52824 88.77515 91.16910
[9] 86.52228 86.77020
> rowMin(tmp5,na.rm=TRUE)
[1] NA 56.65447 61.54621 57.96465 53.50802 57.24452 60.24188 58.70952
[9] 59.07563 54.02380
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 66.85481 70.64490 73.72985 NaN 72.45247 70.01752 73.58927 73.73648
[9] 76.21045 75.31006 66.29848 70.00457 68.44944 71.03290 74.39786 69.39075
[17] 71.18636 75.21216 69.98601 75.47938
> colSums(tmp5,na.rm=TRUE)
[1] 601.6933 635.8041 663.5686 0.0000 652.0723 630.1577 662.3034 663.6283
[9] 685.8941 677.7905 596.6864 630.0412 616.0450 639.2961 669.5808 624.5168
[17] 640.6773 676.9095 629.8741 679.3144
> colVars(tmp5,na.rm=TRUE)
[1] 71.85222 77.94473 61.60173 NA 39.27704 41.38717 145.11653
[8] 40.58286 43.88978 55.66888 86.44579 53.61198 134.00490 83.79271
[15] 148.46325 43.59267 23.41086 42.56278 66.57407 124.65785
> colSd(tmp5,na.rm=TRUE)
[1] 8.476569 8.828631 7.848677 NA 6.267139 6.433286 12.046432
[8] 6.370467 6.624936 7.461158 9.297623 7.322020 11.576049 9.153836
[15] 12.184550 6.602475 4.838477 6.524015 8.159293 11.165028
> colMax(tmp5,na.rm=TRUE)
[1] 79.34415 82.56529 84.85291 -Inf 80.26923 82.50485 96.83644 82.12199
[9] 86.25303 86.74339 78.32731 82.90519 93.52824 88.77515 94.56559 81.48424
[17] 77.61292 88.61258 77.55519 97.93345
> colMin(tmp5,na.rm=TRUE)
[1] 55.03385 57.99943 60.02830 Inf 59.35391 58.70952 56.65447 63.85898
[9] 66.55164 64.91228 53.50802 59.07563 59.51264 57.96465 60.63030 58.93191
[17] 65.30085 68.14065 57.95342 57.24452
>
>
>
>
> 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] 275.2910 182.8057 297.4586 167.8582 229.6081 225.6190 254.3292 202.4990
[9] 254.8864 360.1428
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 275.2910 182.8057 297.4586 167.8582 229.6081 225.6190 254.3292 202.4990
[9] 254.8864 360.1428
>
>
>
> 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] 1.136868e-13 -5.684342e-14 2.842171e-14 5.684342e-14 0.000000e+00
[6] -2.842171e-14 -8.526513e-14 0.000000e+00 -1.421085e-14 -2.415845e-13
[11] -2.842171e-14 -5.684342e-14 -5.684342e-14 -1.421085e-13 -5.684342e-14
[16] -1.989520e-13 -5.684342e-14 -7.105427e-14 0.000000e+00 2.842171e-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)
+ }
4 3
5 5
10 19
8 7
4 5
5 16
8 2
5 8
2 14
2 15
1 19
6 4
6 15
7 18
9 12
2 1
2 6
2 16
10 7
10 8
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] 2.764868
> Min(tmp)
[1] -2.646189
> mean(tmp)
[1] -0.03096842
> Sum(tmp)
[1] -3.096842
> Var(tmp)
[1] 1.118895
>
> rowMeans(tmp)
[1] -0.03096842
> rowSums(tmp)
[1] -3.096842
> rowVars(tmp)
[1] 1.118895
> rowSd(tmp)
[1] 1.057778
> rowMax(tmp)
[1] 2.764868
> rowMin(tmp)
[1] -2.646189
>
> colMeans(tmp)
[1] -1.59933934 -0.31746388 0.89063068 -0.33628160 -0.99481362 -0.38552717
[7] 0.98130959 -0.82951673 -0.27868577 -0.37500880 -0.77293022 1.10009722
[13] 2.07081917 2.76486847 -0.82234606 -0.67290556 -0.04928828 0.45752490
[19] 0.17694230 -0.39583671 0.81339660 1.12329909 -1.74359353 1.26004321
[25] 0.99872554 -1.20437459 -1.90430228 0.44021661 0.08091989 -0.38516566
[31] 0.67028577 -0.78321460 -0.59175275 -1.25177035 0.58658492 1.86964011
[37] 0.25200025 0.10061788 0.64375205 -1.54622178 0.31954770 0.06324175
[43] 0.24991611 -1.24552237 1.22656534 1.38794116 1.29626826 0.68392628
[49] 0.76894687 0.14818606 -0.31150126 1.97260871 2.09194399 -1.29130812
[55] -1.01276516 -0.08849203 -1.25162870 0.82227262 0.18832221 -2.64618919
[61] -1.03433043 1.28809677 0.81197761 -0.33317552 0.61702926 -0.79350987
[67] 1.12501535 -0.57817677 -1.00033555 0.29532284 -0.96946811 -2.07397652
[73] -1.04760269 0.34315226 -0.50693790 -0.88257547 0.58580020 -0.05421366
[79] -0.63536825 1.33622405 -1.08771403 -1.22812118 -0.22311144 0.85207353
[85] 0.55390521 -0.64687508 0.10592198 0.43948487 -1.76948289 -1.20791929
[91] -1.37666797 0.23736708 0.89071922 1.47012831 -0.41327030 -1.86330322
[97] -0.17048076 1.69452695 0.08767168 0.65174277
> colSums(tmp)
[1] -1.59933934 -0.31746388 0.89063068 -0.33628160 -0.99481362 -0.38552717
[7] 0.98130959 -0.82951673 -0.27868577 -0.37500880 -0.77293022 1.10009722
[13] 2.07081917 2.76486847 -0.82234606 -0.67290556 -0.04928828 0.45752490
[19] 0.17694230 -0.39583671 0.81339660 1.12329909 -1.74359353 1.26004321
[25] 0.99872554 -1.20437459 -1.90430228 0.44021661 0.08091989 -0.38516566
[31] 0.67028577 -0.78321460 -0.59175275 -1.25177035 0.58658492 1.86964011
[37] 0.25200025 0.10061788 0.64375205 -1.54622178 0.31954770 0.06324175
[43] 0.24991611 -1.24552237 1.22656534 1.38794116 1.29626826 0.68392628
[49] 0.76894687 0.14818606 -0.31150126 1.97260871 2.09194399 -1.29130812
[55] -1.01276516 -0.08849203 -1.25162870 0.82227262 0.18832221 -2.64618919
[61] -1.03433043 1.28809677 0.81197761 -0.33317552 0.61702926 -0.79350987
[67] 1.12501535 -0.57817677 -1.00033555 0.29532284 -0.96946811 -2.07397652
[73] -1.04760269 0.34315226 -0.50693790 -0.88257547 0.58580020 -0.05421366
[79] -0.63536825 1.33622405 -1.08771403 -1.22812118 -0.22311144 0.85207353
[85] 0.55390521 -0.64687508 0.10592198 0.43948487 -1.76948289 -1.20791929
[91] -1.37666797 0.23736708 0.89071922 1.47012831 -0.41327030 -1.86330322
[97] -0.17048076 1.69452695 0.08767168 0.65174277
> 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] -1.59933934 -0.31746388 0.89063068 -0.33628160 -0.99481362 -0.38552717
[7] 0.98130959 -0.82951673 -0.27868577 -0.37500880 -0.77293022 1.10009722
[13] 2.07081917 2.76486847 -0.82234606 -0.67290556 -0.04928828 0.45752490
[19] 0.17694230 -0.39583671 0.81339660 1.12329909 -1.74359353 1.26004321
[25] 0.99872554 -1.20437459 -1.90430228 0.44021661 0.08091989 -0.38516566
[31] 0.67028577 -0.78321460 -0.59175275 -1.25177035 0.58658492 1.86964011
[37] 0.25200025 0.10061788 0.64375205 -1.54622178 0.31954770 0.06324175
[43] 0.24991611 -1.24552237 1.22656534 1.38794116 1.29626826 0.68392628
[49] 0.76894687 0.14818606 -0.31150126 1.97260871 2.09194399 -1.29130812
[55] -1.01276516 -0.08849203 -1.25162870 0.82227262 0.18832221 -2.64618919
[61] -1.03433043 1.28809677 0.81197761 -0.33317552 0.61702926 -0.79350987
[67] 1.12501535 -0.57817677 -1.00033555 0.29532284 -0.96946811 -2.07397652
[73] -1.04760269 0.34315226 -0.50693790 -0.88257547 0.58580020 -0.05421366
[79] -0.63536825 1.33622405 -1.08771403 -1.22812118 -0.22311144 0.85207353
[85] 0.55390521 -0.64687508 0.10592198 0.43948487 -1.76948289 -1.20791929
[91] -1.37666797 0.23736708 0.89071922 1.47012831 -0.41327030 -1.86330322
[97] -0.17048076 1.69452695 0.08767168 0.65174277
> colMin(tmp)
[1] -1.59933934 -0.31746388 0.89063068 -0.33628160 -0.99481362 -0.38552717
[7] 0.98130959 -0.82951673 -0.27868577 -0.37500880 -0.77293022 1.10009722
[13] 2.07081917 2.76486847 -0.82234606 -0.67290556 -0.04928828 0.45752490
[19] 0.17694230 -0.39583671 0.81339660 1.12329909 -1.74359353 1.26004321
[25] 0.99872554 -1.20437459 -1.90430228 0.44021661 0.08091989 -0.38516566
[31] 0.67028577 -0.78321460 -0.59175275 -1.25177035 0.58658492 1.86964011
[37] 0.25200025 0.10061788 0.64375205 -1.54622178 0.31954770 0.06324175
[43] 0.24991611 -1.24552237 1.22656534 1.38794116 1.29626826 0.68392628
[49] 0.76894687 0.14818606 -0.31150126 1.97260871 2.09194399 -1.29130812
[55] -1.01276516 -0.08849203 -1.25162870 0.82227262 0.18832221 -2.64618919
[61] -1.03433043 1.28809677 0.81197761 -0.33317552 0.61702926 -0.79350987
[67] 1.12501535 -0.57817677 -1.00033555 0.29532284 -0.96946811 -2.07397652
[73] -1.04760269 0.34315226 -0.50693790 -0.88257547 0.58580020 -0.05421366
[79] -0.63536825 1.33622405 -1.08771403 -1.22812118 -0.22311144 0.85207353
[85] 0.55390521 -0.64687508 0.10592198 0.43948487 -1.76948289 -1.20791929
[91] -1.37666797 0.23736708 0.89071922 1.47012831 -0.41327030 -1.86330322
[97] -0.17048076 1.69452695 0.08767168 0.65174277
> colMedians(tmp)
[1] -1.59933934 -0.31746388 0.89063068 -0.33628160 -0.99481362 -0.38552717
[7] 0.98130959 -0.82951673 -0.27868577 -0.37500880 -0.77293022 1.10009722
[13] 2.07081917 2.76486847 -0.82234606 -0.67290556 -0.04928828 0.45752490
[19] 0.17694230 -0.39583671 0.81339660 1.12329909 -1.74359353 1.26004321
[25] 0.99872554 -1.20437459 -1.90430228 0.44021661 0.08091989 -0.38516566
[31] 0.67028577 -0.78321460 -0.59175275 -1.25177035 0.58658492 1.86964011
[37] 0.25200025 0.10061788 0.64375205 -1.54622178 0.31954770 0.06324175
[43] 0.24991611 -1.24552237 1.22656534 1.38794116 1.29626826 0.68392628
[49] 0.76894687 0.14818606 -0.31150126 1.97260871 2.09194399 -1.29130812
[55] -1.01276516 -0.08849203 -1.25162870 0.82227262 0.18832221 -2.64618919
[61] -1.03433043 1.28809677 0.81197761 -0.33317552 0.61702926 -0.79350987
[67] 1.12501535 -0.57817677 -1.00033555 0.29532284 -0.96946811 -2.07397652
[73] -1.04760269 0.34315226 -0.50693790 -0.88257547 0.58580020 -0.05421366
[79] -0.63536825 1.33622405 -1.08771403 -1.22812118 -0.22311144 0.85207353
[85] 0.55390521 -0.64687508 0.10592198 0.43948487 -1.76948289 -1.20791929
[91] -1.37666797 0.23736708 0.89071922 1.47012831 -0.41327030 -1.86330322
[97] -0.17048076 1.69452695 0.08767168 0.65174277
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] -1.599339 -0.3174639 0.8906307 -0.3362816 -0.9948136 -0.3855272 0.9813096
[2,] -1.599339 -0.3174639 0.8906307 -0.3362816 -0.9948136 -0.3855272 0.9813096
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] -0.8295167 -0.2786858 -0.3750088 -0.7729302 1.100097 2.070819 2.764868
[2,] -0.8295167 -0.2786858 -0.3750088 -0.7729302 1.100097 2.070819 2.764868
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] -0.8223461 -0.6729056 -0.04928828 0.4575249 0.1769423 -0.3958367 0.8133966
[2,] -0.8223461 -0.6729056 -0.04928828 0.4575249 0.1769423 -0.3958367 0.8133966
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] 1.123299 -1.743594 1.260043 0.9987255 -1.204375 -1.904302 0.4402166
[2,] 1.123299 -1.743594 1.260043 0.9987255 -1.204375 -1.904302 0.4402166
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] 0.08091989 -0.3851657 0.6702858 -0.7832146 -0.5917527 -1.25177 0.5865849
[2,] 0.08091989 -0.3851657 0.6702858 -0.7832146 -0.5917527 -1.25177 0.5865849
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] 1.86964 0.2520002 0.1006179 0.6437521 -1.546222 0.3195477 0.06324175
[2,] 1.86964 0.2520002 0.1006179 0.6437521 -1.546222 0.3195477 0.06324175
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] 0.2499161 -1.245522 1.226565 1.387941 1.296268 0.6839263 0.7689469
[2,] 0.2499161 -1.245522 1.226565 1.387941 1.296268 0.6839263 0.7689469
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] 0.1481861 -0.3115013 1.972609 2.091944 -1.291308 -1.012765 -0.08849203
[2,] 0.1481861 -0.3115013 1.972609 2.091944 -1.291308 -1.012765 -0.08849203
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] -1.251629 0.8222726 0.1883222 -2.646189 -1.03433 1.288097 0.8119776
[2,] -1.251629 0.8222726 0.1883222 -2.646189 -1.03433 1.288097 0.8119776
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] -0.3331755 0.6170293 -0.7935099 1.125015 -0.5781768 -1.000336 0.2953228
[2,] -0.3331755 0.6170293 -0.7935099 1.125015 -0.5781768 -1.000336 0.2953228
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] -0.9694681 -2.073977 -1.047603 0.3431523 -0.5069379 -0.8825755 0.5858002
[2,] -0.9694681 -2.073977 -1.047603 0.3431523 -0.5069379 -0.8825755 0.5858002
[,78] [,79] [,80] [,81] [,82] [,83] [,84]
[1,] -0.05421366 -0.6353682 1.336224 -1.087714 -1.228121 -0.2231114 0.8520735
[2,] -0.05421366 -0.6353682 1.336224 -1.087714 -1.228121 -0.2231114 0.8520735
[,85] [,86] [,87] [,88] [,89] [,90] [,91]
[1,] 0.5539052 -0.6468751 0.105922 0.4394849 -1.769483 -1.207919 -1.376668
[2,] 0.5539052 -0.6468751 0.105922 0.4394849 -1.769483 -1.207919 -1.376668
[,92] [,93] [,94] [,95] [,96] [,97] [,98]
[1,] 0.2373671 0.8907192 1.470128 -0.4132703 -1.863303 -0.1704808 1.694527
[2,] 0.2373671 0.8907192 1.470128 -0.4132703 -1.863303 -0.1704808 1.694527
[,99] [,100]
[1,] 0.08767168 0.6517428
[2,] 0.08767168 0.6517428
>
>
> Max(tmp2)
[1] 1.601196
> Min(tmp2)
[1] -1.851209
> mean(tmp2)
[1] -0.05548475
> Sum(tmp2)
[1] -5.548475
> Var(tmp2)
[1] 0.6468287
>
> rowMeans(tmp2)
[1] -1.037086278 0.240266998 -0.633438521 -0.335904664 0.149134139
[6] -0.344278416 0.713909014 -0.179908062 0.055374942 0.768996924
[11] -1.043246396 0.217299184 0.591778690 -0.722654025 1.601196183
[16] 0.966743981 -0.750014597 -0.156512779 0.569448175 0.427597190
[21] -1.329894093 0.364102065 0.352477248 0.737490777 -0.009615697
[26] -1.851208911 -0.825680055 1.048708441 0.155677563 -0.565999254
[31] -0.091929157 0.026913356 -0.240422895 1.482002482 -0.018175911
[36] -1.778006280 1.116354823 -0.626351927 -0.256966997 -1.694698667
[41] 0.950883822 0.774975721 -0.251560897 0.382650588 -1.726137271
[46] -0.469286968 0.194880839 0.791421035 0.741838606 -0.678580974
[51] -0.141412843 0.866904911 -0.125081592 -0.868148198 -1.707024084
[56] 0.909691153 -0.688517464 -1.788802921 -1.051553503 -0.779776348
[61] 0.624308538 0.215915685 -0.600948889 0.443678849 -0.625722480
[66] -0.923200566 0.116202489 -1.100111903 -0.755670620 0.040047909
[71] 0.596960620 0.675987178 1.548066208 -0.888451846 0.547446527
[76] 0.253546034 -1.084438850 0.412469426 0.064120517 0.203351756
[81] -1.088450430 -0.396853093 -0.029803709 1.054287130 0.355641550
[86] -0.863504134 0.104909519 -0.618125290 0.858109636 -0.549245340
[91] 0.735603644 0.843187083 -0.199743528 1.112463367 0.521074360
[96] -0.963314324 0.964383109 0.394580716 -0.180215151 0.202140696
> rowSums(tmp2)
[1] -1.037086278 0.240266998 -0.633438521 -0.335904664 0.149134139
[6] -0.344278416 0.713909014 -0.179908062 0.055374942 0.768996924
[11] -1.043246396 0.217299184 0.591778690 -0.722654025 1.601196183
[16] 0.966743981 -0.750014597 -0.156512779 0.569448175 0.427597190
[21] -1.329894093 0.364102065 0.352477248 0.737490777 -0.009615697
[26] -1.851208911 -0.825680055 1.048708441 0.155677563 -0.565999254
[31] -0.091929157 0.026913356 -0.240422895 1.482002482 -0.018175911
[36] -1.778006280 1.116354823 -0.626351927 -0.256966997 -1.694698667
[41] 0.950883822 0.774975721 -0.251560897 0.382650588 -1.726137271
[46] -0.469286968 0.194880839 0.791421035 0.741838606 -0.678580974
[51] -0.141412843 0.866904911 -0.125081592 -0.868148198 -1.707024084
[56] 0.909691153 -0.688517464 -1.788802921 -1.051553503 -0.779776348
[61] 0.624308538 0.215915685 -0.600948889 0.443678849 -0.625722480
[66] -0.923200566 0.116202489 -1.100111903 -0.755670620 0.040047909
[71] 0.596960620 0.675987178 1.548066208 -0.888451846 0.547446527
[76] 0.253546034 -1.084438850 0.412469426 0.064120517 0.203351756
[81] -1.088450430 -0.396853093 -0.029803709 1.054287130 0.355641550
[86] -0.863504134 0.104909519 -0.618125290 0.858109636 -0.549245340
[91] 0.735603644 0.843187083 -0.199743528 1.112463367 0.521074360
[96] -0.963314324 0.964383109 0.394580716 -0.180215151 0.202140696
> 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] -1.037086278 0.240266998 -0.633438521 -0.335904664 0.149134139
[6] -0.344278416 0.713909014 -0.179908062 0.055374942 0.768996924
[11] -1.043246396 0.217299184 0.591778690 -0.722654025 1.601196183
[16] 0.966743981 -0.750014597 -0.156512779 0.569448175 0.427597190
[21] -1.329894093 0.364102065 0.352477248 0.737490777 -0.009615697
[26] -1.851208911 -0.825680055 1.048708441 0.155677563 -0.565999254
[31] -0.091929157 0.026913356 -0.240422895 1.482002482 -0.018175911
[36] -1.778006280 1.116354823 -0.626351927 -0.256966997 -1.694698667
[41] 0.950883822 0.774975721 -0.251560897 0.382650588 -1.726137271
[46] -0.469286968 0.194880839 0.791421035 0.741838606 -0.678580974
[51] -0.141412843 0.866904911 -0.125081592 -0.868148198 -1.707024084
[56] 0.909691153 -0.688517464 -1.788802921 -1.051553503 -0.779776348
[61] 0.624308538 0.215915685 -0.600948889 0.443678849 -0.625722480
[66] -0.923200566 0.116202489 -1.100111903 -0.755670620 0.040047909
[71] 0.596960620 0.675987178 1.548066208 -0.888451846 0.547446527
[76] 0.253546034 -1.084438850 0.412469426 0.064120517 0.203351756
[81] -1.088450430 -0.396853093 -0.029803709 1.054287130 0.355641550
[86] -0.863504134 0.104909519 -0.618125290 0.858109636 -0.549245340
[91] 0.735603644 0.843187083 -0.199743528 1.112463367 0.521074360
[96] -0.963314324 0.964383109 0.394580716 -0.180215151 0.202140696
> rowMin(tmp2)
[1] -1.037086278 0.240266998 -0.633438521 -0.335904664 0.149134139
[6] -0.344278416 0.713909014 -0.179908062 0.055374942 0.768996924
[11] -1.043246396 0.217299184 0.591778690 -0.722654025 1.601196183
[16] 0.966743981 -0.750014597 -0.156512779 0.569448175 0.427597190
[21] -1.329894093 0.364102065 0.352477248 0.737490777 -0.009615697
[26] -1.851208911 -0.825680055 1.048708441 0.155677563 -0.565999254
[31] -0.091929157 0.026913356 -0.240422895 1.482002482 -0.018175911
[36] -1.778006280 1.116354823 -0.626351927 -0.256966997 -1.694698667
[41] 0.950883822 0.774975721 -0.251560897 0.382650588 -1.726137271
[46] -0.469286968 0.194880839 0.791421035 0.741838606 -0.678580974
[51] -0.141412843 0.866904911 -0.125081592 -0.868148198 -1.707024084
[56] 0.909691153 -0.688517464 -1.788802921 -1.051553503 -0.779776348
[61] 0.624308538 0.215915685 -0.600948889 0.443678849 -0.625722480
[66] -0.923200566 0.116202489 -1.100111903 -0.755670620 0.040047909
[71] 0.596960620 0.675987178 1.548066208 -0.888451846 0.547446527
[76] 0.253546034 -1.084438850 0.412469426 0.064120517 0.203351756
[81] -1.088450430 -0.396853093 -0.029803709 1.054287130 0.355641550
[86] -0.863504134 0.104909519 -0.618125290 0.858109636 -0.549245340
[91] 0.735603644 0.843187083 -0.199743528 1.112463367 0.521074360
[96] -0.963314324 0.964383109 0.394580716 -0.180215151 0.202140696
>
> colMeans(tmp2)
[1] -0.05548475
> colSums(tmp2)
[1] -5.548475
> colVars(tmp2)
[1] 0.6468287
> colSd(tmp2)
[1] 0.8042566
> colMax(tmp2)
[1] 1.601196
> colMin(tmp2)
[1] -1.851209
> colMedians(tmp2)
[1] 0.03348063
> colRanges(tmp2)
[,1]
[1,] -1.851209
[2,] 1.601196
>
> 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] -1.7670394 -4.1953282 -2.0857988 -1.6435723 1.0090192 0.6359393
[7] -3.7964479 3.1907512 -4.0837046 4.4354551
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.5602274
[2,] -0.6135518
[3,] -0.3742608
[4,] 0.2106096
[5,] 1.9507003
>
> rowApply(tmp,sum)
[1] -1.4396571 3.0928010 -0.8721670 -4.2082354 -7.4737417 0.4375002
[7] -1.8156663 1.2562877 2.2747659 0.4473864
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 10 6 3 4 3 7 3 3 3 5
[2,] 4 4 6 3 8 6 1 6 1 3
[3,] 3 7 5 1 1 5 10 5 5 8
[4,] 6 9 9 5 5 9 2 1 4 6
[5,] 7 5 4 2 2 8 4 4 10 10
[6,] 8 8 1 6 10 4 5 8 7 2
[7,] 5 1 7 7 9 2 6 2 8 1
[8,] 2 3 8 10 4 10 7 7 9 7
[9,] 1 2 2 8 7 1 9 9 2 9
[10,] 9 10 10 9 6 3 8 10 6 4
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] 0.8989826 1.4565799 0.6647762 -1.0671232 2.0082873 -1.3803330
[7] 1.7445585 -1.9692745 -1.2521170 -1.0715824 1.4923179 -0.2088551
[13] -3.3509293 0.6440985 -0.9978883 -2.3878297 -0.1733217 3.5035970
[19] -1.6455032 2.3411744
> colApply(tmp,quantile)[,1]
[,1]
[1,] -2.1057712
[2,] -0.6478774
[3,] 0.6683324
[4,] 1.4651951
[5,] 1.5191036
>
> rowApply(tmp,sum)
[1] 0.1490922 -3.2399674 -6.1198950 1.6798207 6.7805643
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 4 1 19 20 13
[2,] 9 20 13 15 7
[3,] 18 10 6 12 11
[4,] 15 3 10 3 20
[5,] 17 19 3 8 19
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] -0.6478774 -0.30075349 0.86393322 0.5236892 0.768402555 0.16673968
[2,] -2.1057712 1.45684750 -0.04417085 -1.1806509 1.404348313 -0.97496355
[3,] 1.4651951 -0.27304566 -1.13321976 -0.6547146 -1.528503839 -1.80188479
[4,] 1.5191036 0.49076864 0.35502101 -1.3349604 -0.007084613 -0.09606911
[5,] 0.6683324 0.08276293 0.62321254 1.5795135 1.371124922 1.32584477
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] -0.03645211 -0.38235441 -0.1986954 -1.538012378 -0.3714111 -0.3425135
[2,] -0.50792535 0.19995677 -2.0352085 -0.008940197 -0.7023399 1.0520075
[3,] 0.45093636 -1.02080225 0.6313277 0.073090464 2.8912003 -0.6593108
[4,] 1.20252276 0.07841219 0.0319593 1.464208735 -0.7119619 0.1317462
[5,] 0.63547688 -0.84448681 0.3185000 -1.061929008 0.3868304 -0.3907846
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] -1.1230275 0.07064914 0.58301759 -0.4148296 -1.3984932 -0.2839975
[2,] -1.1138961 0.46566436 -0.01432546 -0.6660424 0.6819051 0.6047595
[3,] -0.4639354 -1.21570151 -0.71357427 -0.6191291 0.7530414 1.0026215
[4,] -0.4207559 0.39009895 -1.61667373 -1.0295488 0.4033265 1.3536956
[5,] -0.2293144 0.93338754 0.76366758 0.3417202 -0.6131014 0.8265179
[,19] [,20]
[1,] 1.0717149 3.1393636
[2,] -0.9409822 1.1897602
[3,] -1.3770010 -1.9264849
[4,] -1.3384791 0.8144908
[5,] 0.9392443 -0.8759554
>
>
> is.BufferedMatrix(tmp)
[1] TRUE
>
> as.BufferedMatrix(as.matrix(tmp))
BufferedMatrix object
Matrix size: 5 20
Buffer size: 1 1
Directory: /home/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: /home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 652 bytes.
Disk usage : 200 bytes.
> subBufferedMatrix(tmp,,5:8)
BufferedMatrix object
Matrix size: 5 4
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 566 bytes.
Disk usage : 160 bytes.
> subBufferedMatrix(tmp,1:3,)
BufferedMatrix object
Matrix size: 3 20
Buffer size: 1 1
Directory: /home/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 -0.4748373 0.5234322 1.05875 -0.804001 0.992267 -0.1183741 0.2995929
col8 col9 col10 col11 col12 col13 col14
row1 -0.2208304 -0.7082607 0.3993855 -0.7629808 1.010256 -0.2834571 1.025899
col15 col16 col17 col18 col19 col20
row1 -0.7065811 1.540417 0.5028013 -0.9000262 -1.178413 0.59098
> tmp[,"col10"]
col10
row1 0.3993855
row2 0.6597771
row3 -0.4626832
row4 0.7776508
row5 0.1161789
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7
row1 -0.4748373 0.5234322 1.058750 -0.8040010 0.9922670 -0.1183741 0.2995929
row5 -0.8608215 0.1971571 1.379715 -0.6740401 0.1620005 -0.5002252 -0.2606803
col8 col9 col10 col11 col12 col13 col14
row1 -0.2208304 -0.7082607 0.3993855 -0.76298078 1.010256 -0.2834571 1.0258989
row5 0.1217673 0.7160417 0.1161789 0.04853684 1.185178 0.5792923 0.3533421
col15 col16 col17 col18 col19 col20
row1 -0.70658112 1.540417 0.5028013 -0.9000262 -1.178413 0.590980
row5 0.02066107 1.280540 0.7560541 -0.7497993 1.132668 1.542649
> tmp[,c("col6","col20")]
col6 col20
row1 -0.1183741 0.5909800
row2 -0.2166778 0.5166806
row3 1.6352649 -0.5812306
row4 1.5764971 -0.2717820
row5 -0.5002252 1.5426489
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 -0.1183741 0.590980
row5 -0.5002252 1.542649
>
>
>
>
> 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 49.23162 50.03553 50.17413 49.80272 50.29958 105.0825 50.25811 49.13307
col9 col10 col11 col12 col13 col14 col15 col16
row1 51.34664 50.40622 50.88618 50.40962 49.8818 51.67405 49.33847 49.57418
col17 col18 col19 col20
row1 50.40212 50.61332 49.20023 106.7015
> tmp[,"col10"]
col10
row1 50.40622
row2 29.43418
row3 28.66074
row4 29.78078
row5 48.92361
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 49.23162 50.03553 50.17413 49.80272 50.29958 105.0825 50.25811 49.13307
row5 50.15581 48.96706 50.23938 48.96036 49.39468 103.4656 50.07075 49.83842
col9 col10 col11 col12 col13 col14 col15 col16
row1 51.34664 50.40622 50.88618 50.40962 49.88180 51.67405 49.33847 49.57418
row5 50.30217 48.92361 50.10928 50.60553 50.02404 50.75663 49.70968 50.89944
col17 col18 col19 col20
row1 50.40212 50.61332 49.20023 106.7015
row5 49.23159 50.45965 50.53481 102.9818
> tmp[,c("col6","col20")]
col6 col20
row1 105.08248 106.70150
row2 74.49015 73.19948
row3 74.63015 76.01161
row4 75.11459 74.27775
row5 103.46564 102.98181
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 105.0825 106.7015
row5 103.4656 102.9818
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 105.0825 106.7015
row5 103.4656 102.9818
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] -0.46681579
[2,] 0.01336921
[3,] -1.04114324
[4,] -2.00711284
[5,] 0.69368598
> tmp[,c("col17","col7")]
col17 col7
[1,] -0.93155760 1.0730621
[2,] 1.21621210 -0.9741544
[3,] -1.01414110 1.4070284
[4,] -0.04984183 -0.0931999
[5,] -0.73091982 -0.1684545
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] -0.5414838 -0.08709579
[2,] -1.5622632 0.57922904
[3,] 1.1338358 -0.89316834
[4,] 0.8681758 -0.01388961
[5,] 0.9157880 -0.54082815
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] -0.5414838
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] -0.5414838
[2,] -1.5622632
>
>
>
> 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] [,7]
row3 -1.1598505 0.7789490 0.8164875 -1.090600 1.4845401 -1.621301 0.1783246
row1 0.7569913 0.2872144 -0.6226832 1.033765 0.2735822 1.818367 -1.0792553
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row3 -1.0786804 1.956105 1.340506 -1.786616 -0.3383109 1.310397 0.99681679
row1 -0.3408295 -0.213272 0.236658 -1.309128 -0.8863597 -2.066580 0.08998083
[,15] [,16] [,17] [,18] [,19] [,20]
row3 1.337391 -2.649677 0.233197 1.1989532 -0.2829885 1.693370
row1 -1.353423 -1.285064 -1.627476 0.9005792 -0.6217863 0.121298
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 0.6203542 -0.3750584 -0.5392414 -0.4498806 -1.991409 -0.6161807 0.2769299
[,8] [,9] [,10]
row2 -0.6569875 -0.6184937 0.005864714
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 0.1156895 -0.5979248 0.7633919 -0.9205637 2.193276 -0.7402234 -1.125422
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 -0.2060966 -1.105155 0.5659864 1.412838 -0.7799442 -0.1759786 1.771747
[,15] [,16] [,17] [,18] [,19] [,20]
row5 -1.247402 -0.3358135 -0.6371186 -0.6677512 -1.758485 -1.06276
>
>
> 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: 0x61c2021c88b0>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM1ca14a71828c7f"
[2] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM1ca14a3371f0f4"
[3] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM1ca14a3b47b202"
[4] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM1ca14a6ae79172"
[5] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM1ca14a37c876d1"
[6] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM1ca14a2e278cee"
[7] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM1ca14a623c30f0"
[8] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM1ca14a5e4ea48b"
[9] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM1ca14a4d17a17c"
[10] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM1ca14a37370df4"
[11] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM1ca14a5a7db547"
[12] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM1ca14a767caac8"
[13] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM1ca14a1b8cc6a3"
[14] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM1ca14a52ce20b5"
[15] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM1ca14a169bc7d1"
>
>
> ### 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: 0x61c201bf59a0>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x61c201bf59a0>
Warning message:
In dir.create(new.directory) :
'/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x61c201bf59a0>
> rowMedians(tmp)
[1] 0.431688092 -0.383415540 -0.192364899 0.053808312 0.258721600
[6] 0.410529140 -0.112976375 -0.081111280 0.039178703 -0.255137169
[11] 0.037537923 0.061067843 -0.206256315 -0.315769278 -0.016586437
[16] -0.482547838 -0.138077679 -0.186047057 -0.171834150 -0.055479460
[21] 0.300472398 -0.326853460 0.220486864 -0.520418442 0.273380402
[26] -0.396637283 0.256460825 -0.602166862 0.145062352 -0.062545011
[31] 0.268144052 0.116485342 -0.172231743 -0.483309539 -0.233798485
[36] -0.159780572 -0.547532245 -0.162287767 -0.439812756 0.275886451
[41] -0.425686375 -0.161833306 -0.443049114 0.088097545 0.109856179
[46] 0.140236141 -0.320410335 -0.148550897 0.017600276 0.383215442
[51] -0.105941126 -0.332052096 0.087997287 -0.260832912 0.363558549
[56] -0.345164848 0.182480907 -0.389763289 0.003605743 -0.432845342
[61] -0.810432777 0.125373818 -0.385967141 0.490175128 -0.141339922
[66] -0.032844301 -0.147623987 0.257844282 0.248578156 -0.445983405
[71] 0.205722583 -0.051123729 -0.196760873 -0.830328555 -0.709502263
[76] -0.167318142 0.463507364 -0.059939680 -0.378518838 0.277024321
[81] 0.900043610 0.139795895 0.102698086 -0.116355983 0.016514118
[86] -0.635589528 0.097721120 0.214754513 0.121647049 0.234677362
[91] -0.100856404 -0.004797388 -0.060805671 0.182667727 -0.481199298
[96] -0.251526559 0.596959327 -0.408910298 -0.269416199 0.225213617
[101] 0.115015565 0.483501042 0.133150781 0.388822605 -0.181368522
[106] 0.155105754 -0.170613509 -0.584077777 -0.291919703 0.296449132
[111] -0.107444178 -0.168627580 -0.033795557 -0.187520630 0.150749925
[116] 0.149442378 0.653005207 -0.646234888 -0.354084710 -0.521563735
[121] -0.141996479 -0.267536388 0.070553498 0.081181477 -0.130403470
[126] -0.225851069 0.009287671 -0.194510689 -0.135180662 -0.244731607
[131] -0.252072625 -0.133744609 -0.025104696 -0.208917895 -0.564102897
[136] 0.145030159 -0.011588584 0.221458033 0.049892535 -0.270132617
[141] 0.199337146 0.454629827 -0.015852412 -0.185503480 -0.235952335
[146] 0.001763020 0.519970859 0.233445814 0.613717531 0.144617208
[151] -0.203934596 -0.001109759 0.140307833 0.242471299 -0.359215768
[156] -0.327739167 -0.311888542 -0.561575594 -0.469534571 -0.232156402
[161] 0.118066289 0.128154057 0.510668999 -0.301074081 0.164217434
[166] 0.281421260 -0.392886800 -0.568989888 0.271523678 -0.189755246
[171] -0.124052567 0.323571738 -0.067109790 -0.627570833 -0.526408156
[176] -0.347028101 -0.011677714 0.113921933 0.583749992 0.194388119
[181] 0.443549985 0.008981113 0.312789899 0.478941565 0.371565305
[186] 0.176890841 -0.161528658 0.530576688 0.114492150 0.405385400
[191] -0.103559498 -0.125539440 0.293879394 -0.326032836 0.010608309
[196] -0.102357987 0.079788832 -0.082474716 0.300508052 -0.045537068
[201] 0.200736577 -0.273664262 0.422211374 0.344466887 -0.018451914
[206] 0.569222378 -0.475114727 -0.144788088 -0.500066700 -0.138057047
[211] -0.090453831 0.390165405 0.083699747 0.345267858 0.443468074
[216] 0.124935575 -0.261279456 -0.187908066 0.310392641 0.511083719
[221] 0.260485748 0.085765986 -0.447408343 -0.367031259 0.464788398
[226] -0.176498655 0.058595169 -0.239750027 0.001836498 -0.218432322
>
> proc.time()
user system elapsed
1.298 1.443 2.730
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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: 0x5b1e60e86ff0>
> .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: 0x5b1e60e86ff0>
> .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: 0x5b1e60e86ff0>
> .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: 0x5b1e60e86ff0>
> 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: 0x5b1e60b32710>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5b1e60b32710>
> .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: 0x5b1e60b32710>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5b1e60b32710>
> .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: 0x5b1e60b32710>
> 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: 0x5b1e60e963f0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5b1e60e963f0>
> .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: 0x5b1e60e963f0>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x5b1e60e963f0>
> .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: 0x5b1e60e963f0>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x5b1e60e963f0>
> .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: 0x5b1e60e963f0>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x5b1e60e963f0>
> .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: 0x5b1e60e963f0>
> 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: 0x5b1e605cd8c0>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x5b1e605cd8c0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5b1e605cd8c0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5b1e605cd8c0>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile1ca1f3151b7e61" "BufferedMatrixFile1ca1f34e6d12a"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile1ca1f3151b7e61" "BufferedMatrixFile1ca1f34e6d12a"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x5b1e602f9e30>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5b1e602f9e30>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x5b1e602f9e30>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x5b1e602f9e30>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x5b1e602f9e30>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x5b1e602f9e30>
> .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: 0x5b1e61455790>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5b1e61455790>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x5b1e61455790>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x5b1e61455790>
> 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: 0x5b1e60840860>
> .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: 0x5b1e60840860>
> rm(P)
>
> proc.time()
user system elapsed
0.242 0.049 0.281
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences"
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Platform: x86_64-pc-linux-gnu
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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
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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
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> 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
0.246 0.038 0.270