Ben Bolstad
| Snapshot Date: 2026-04-21 14:59 -0400 (Tue, 21 Apr 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 Build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-04-22 11:57 -0400 (Wed, 22 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4796 |
| 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 249/2351 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BufferedMatrix 1.75.0 (landing page) Ben Bolstad
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| 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-3.24-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings BufferedMatrix_1.75.0.tar.gz |
| StartedAt: 2026-04-21 22:27:46 -0400 (Tue, 21 Apr 2026) |
| EndedAt: 2026-04-21 22:28:10 -0400 (Tue, 21 Apr 2026) |
| EllapsedTime: 24.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 0 |
##############################################################################
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### Running command:
###
### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings BufferedMatrix_1.75.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-22 02:27:46 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-3.24-bioc/meat/BufferedMatrix.Rcheck/00check.log’
for details.
BufferedMatrix.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL BufferedMatrix
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.24-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-3.24-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-3.24-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-3.24-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-3.24-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-3.24-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-3.24-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.24-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 version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
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
0.257 0.042 0.288
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
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-3.24-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 480233 25.7 1053308 56.3 637571 34.1
Vcells 887253 6.8 8388608 64.0 2083896 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] "Tue Apr 21 22:28:01 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] "Tue Apr 21 22:28:01 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: 0x648bc80ab520>
>
>
>
> 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 Apr 21 22:28:02 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] "Tue Apr 21 22:28:02 2026"
>
> ColMode(tmp2)
<pointer: 0x648bc80ab520>
>
>
>
> ### 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,] 98.6414916 1.2479261 0.27916490 -1.6294996
[2,] 0.6260028 -0.4333539 0.08479309 -0.6533520
[3,] 0.9735015 1.0628269 -0.85146613 0.7421449
[4,] 1.5289008 0.1840108 2.01402656 0.8567364
> ewApply(tmp5,abs)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.24-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,] 98.6414916 1.2479261 0.27916490 1.6294996
[2,] 0.6260028 0.4333539 0.08479309 0.6533520
[3,] 0.9735015 1.0628269 0.85146613 0.7421449
[4,] 1.5289008 0.1840108 2.01402656 0.8567364
> ewApply(tmp5,sqrt)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.24-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,] 9.9318423 1.1171061 0.5283606 1.2765185
[2,] 0.7912034 0.6582962 0.2911925 0.8083019
[3,] 0.9866618 1.0309350 0.9227492 0.8614783
[4,] 1.2364873 0.4289648 1.4191640 0.9256006
>
> 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-3.24-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,] 222.95991 37.41899 30.56277 39.39469
[2,] 33.53804 32.01632 27.99672 33.73637
[3,] 35.84012 36.37218 35.07896 34.35693
[4,] 38.89377 29.47366 41.20567 35.11274
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x648bc98a49d0>
> exp(tmp5)
<pointer: 0x648bc98a49d0>
> log(tmp5,2)
<pointer: 0x648bc98a49d0>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 464.0619
> Min(tmp5)
[1] 53.93708
> mean(tmp5)
[1] 74.03432
> Sum(tmp5)
[1] 14806.86
> Var(tmp5)
[1] 836.1864
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 92.38148 70.08046 73.84104 73.49325 72.23847 69.11648 75.24916 69.19010
[9] 71.59404 73.15870
> rowSums(tmp5)
[1] 1847.630 1401.609 1476.821 1469.865 1444.769 1382.330 1504.983 1383.802
[9] 1431.881 1463.174
> rowVars(tmp5)
[1] 7705.80854 68.54568 53.39904 76.45945 46.49683 58.17965
[7] 76.04307 86.72649 58.54475 94.42662
> rowSd(tmp5)
[1] 87.782735 8.279232 7.307465 8.744109 6.818858 7.627559 8.720268
[8] 9.312706 7.651454 9.717336
> rowMax(tmp5)
[1] 464.06185 87.82239 86.90706 87.28831 85.15664 84.31931 92.64372
[8] 88.28482 87.11098 97.54408
> rowMin(tmp5)
[1] 59.86809 54.93617 62.56190 60.34213 58.49987 55.54634 59.26666 53.93708
[9] 59.83844 59.12080
>
> colMeans(tmp5)
[1] 110.97629 71.96889 73.76502 76.65710 69.67718 73.54694 71.94378
[8] 72.93348 72.62619 74.38107 71.60667 68.11159 71.05676 71.63414
[15] 70.68536 73.82181 73.25207 72.77156 74.68766 64.58279
> colSums(tmp5)
[1] 1109.7629 719.6889 737.6502 766.5710 696.7718 735.4694 719.4378
[8] 729.3348 726.2619 743.8107 716.0667 681.1159 710.5676 716.3414
[15] 706.8536 738.2181 732.5207 727.7156 746.8766 645.8279
> colVars(tmp5)
[1] 15458.76658 57.88133 106.52248 82.69720 47.67187 94.09354
[7] 37.81753 65.41554 40.01026 103.76826 42.96731 35.23758
[13] 128.98124 120.02037 25.41439 84.57698 48.93532 63.64896
[19] 52.88618 56.52000
> colSd(tmp5)
[1] 124.333288 7.607978 10.320973 9.093800 6.904482 9.700182
[7] 6.149596 8.087987 6.325366 10.186671 6.554945 5.936125
[13] 11.356991 10.955381 5.041269 9.196574 6.995378 7.978030
[19] 7.272288 7.517978
> colMax(tmp5)
[1] 464.06185 81.58845 88.28482 97.54408 81.03897 92.09251 83.97702
[8] 86.31713 79.37244 96.45366 80.90016 77.50486 87.82239 92.64372
[15] 79.75514 87.11098 84.83747 84.39501 87.28831 75.69596
> colMin(tmp5)
[1] 59.83844 61.34556 58.27150 67.74011 58.93872 60.32313 60.60942 62.69280
[9] 63.77181 59.49477 59.26666 59.12080 53.93708 56.82137 63.34598 61.08431
[17] 62.85611 58.26357 64.32271 54.93617
>
>
> ### 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] 92.38148 70.08046 73.84104 73.49325 NA 69.11648 75.24916 69.19010
[9] 71.59404 73.15870
> rowSums(tmp5)
[1] 1847.630 1401.609 1476.821 1469.865 NA 1382.330 1504.983 1383.802
[9] 1431.881 1463.174
> rowVars(tmp5)
[1] 7705.80854 68.54568 53.39904 76.45945 38.04203 58.17965
[7] 76.04307 86.72649 58.54475 94.42662
> rowSd(tmp5)
[1] 87.782735 8.279232 7.307465 8.744109 6.167822 7.627559 8.720268
[8] 9.312706 7.651454 9.717336
> rowMax(tmp5)
[1] 464.06185 87.82239 86.90706 87.28831 NA 84.31931 92.64372
[8] 88.28482 87.11098 97.54408
> rowMin(tmp5)
[1] 59.86809 54.93617 62.56190 60.34213 NA 55.54634 59.26666 53.93708
[9] 59.83844 59.12080
>
> colMeans(tmp5)
[1] 110.97629 71.96889 73.76502 76.65710 69.67718 73.54694 71.94378
[8] 72.93348 72.62619 74.38107 71.60667 68.11159 NA 71.63414
[15] 70.68536 73.82181 73.25207 72.77156 74.68766 64.58279
> colSums(tmp5)
[1] 1109.7629 719.6889 737.6502 766.5710 696.7718 735.4694 719.4378
[8] 729.3348 726.2619 743.8107 716.0667 681.1159 NA 716.3414
[15] 706.8536 738.2181 732.5207 727.7156 746.8766 645.8279
> colVars(tmp5)
[1] 15458.76658 57.88133 106.52248 82.69720 47.67187 94.09354
[7] 37.81753 65.41554 40.01026 103.76826 42.96731 35.23758
[13] NA 120.02037 25.41439 84.57698 48.93532 63.64896
[19] 52.88618 56.52000
> colSd(tmp5)
[1] 124.333288 7.607978 10.320973 9.093800 6.904482 9.700182
[7] 6.149596 8.087987 6.325366 10.186671 6.554945 5.936125
[13] NA 10.955381 5.041269 9.196574 6.995378 7.978030
[19] 7.272288 7.517978
> colMax(tmp5)
[1] 464.06185 81.58845 88.28482 97.54408 81.03897 92.09251 83.97702
[8] 86.31713 79.37244 96.45366 80.90016 77.50486 NA 92.64372
[15] 79.75514 87.11098 84.83747 84.39501 87.28831 75.69596
> colMin(tmp5)
[1] 59.83844 61.34556 58.27150 67.74011 58.93872 60.32313 60.60942 62.69280
[9] 63.77181 59.49477 59.26666 59.12080 NA 56.82137 63.34598 61.08431
[17] 62.85611 58.26357 64.32271 54.93617
>
> Max(tmp5,na.rm=TRUE)
[1] 464.0619
> Min(tmp5,na.rm=TRUE)
[1] 53.93708
> mean(tmp5,na.rm=TRUE)
[1] 74.11238
> Sum(tmp5,na.rm=TRUE)
[1] 14748.36
> Var(tmp5,na.rm=TRUE)
[1] 839.1846
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 92.38148 70.08046 73.84104 73.49325 72.96155 69.11648 75.24916 69.19010
[9] 71.59404 73.15870
> rowSums(tmp5,na.rm=TRUE)
[1] 1847.630 1401.609 1476.821 1469.865 1386.269 1382.330 1504.983 1383.802
[9] 1431.881 1463.174
> rowVars(tmp5,na.rm=TRUE)
[1] 7705.80854 68.54568 53.39904 76.45945 38.04203 58.17965
[7] 76.04307 86.72649 58.54475 94.42662
> rowSd(tmp5,na.rm=TRUE)
[1] 87.782735 8.279232 7.307465 8.744109 6.167822 7.627559 8.720268
[8] 9.312706 7.651454 9.717336
> rowMax(tmp5,na.rm=TRUE)
[1] 464.06185 87.82239 86.90706 87.28831 85.15664 84.31931 92.64372
[8] 88.28482 87.11098 97.54408
> rowMin(tmp5,na.rm=TRUE)
[1] 59.86809 54.93617 62.56190 60.34213 58.93872 55.54634 59.26666 53.93708
[9] 59.83844 59.12080
>
> colMeans(tmp5,na.rm=TRUE)
[1] 110.97629 71.96889 73.76502 76.65710 69.67718 73.54694 71.94378
[8] 72.93348 72.62619 74.38107 71.60667 68.11159 72.45198 71.63414
[15] 70.68536 73.82181 73.25207 72.77156 74.68766 64.58279
> colSums(tmp5,na.rm=TRUE)
[1] 1109.7629 719.6889 737.6502 766.5710 696.7718 735.4694 719.4378
[8] 729.3348 726.2619 743.8107 716.0667 681.1159 652.0678 716.3414
[15] 706.8536 738.2181 732.5207 727.7156 746.8766 645.8279
> colVars(tmp5,na.rm=TRUE)
[1] 15458.76658 57.88133 106.52248 82.69720 47.67187 94.09354
[7] 37.81753 65.41554 40.01026 103.76826 42.96731 35.23758
[13] 123.20451 120.02037 25.41439 84.57698 48.93532 63.64896
[19] 52.88618 56.52000
> colSd(tmp5,na.rm=TRUE)
[1] 124.333288 7.607978 10.320973 9.093800 6.904482 9.700182
[7] 6.149596 8.087987 6.325366 10.186671 6.554945 5.936125
[13] 11.099753 10.955381 5.041269 9.196574 6.995378 7.978030
[19] 7.272288 7.517978
> colMax(tmp5,na.rm=TRUE)
[1] 464.06185 81.58845 88.28482 97.54408 81.03897 92.09251 83.97702
[8] 86.31713 79.37244 96.45366 80.90016 77.50486 87.82239 92.64372
[15] 79.75514 87.11098 84.83747 84.39501 87.28831 75.69596
> colMin(tmp5,na.rm=TRUE)
[1] 59.83844 61.34556 58.27150 67.74011 58.93872 60.32313 60.60942 62.69280
[9] 63.77181 59.49477 59.26666 59.12080 53.93708 56.82137 63.34598 61.08431
[17] 62.85611 58.26357 64.32271 54.93617
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 92.38148 70.08046 73.84104 73.49325 NaN 69.11648 75.24916 69.19010
[9] 71.59404 73.15870
> rowSums(tmp5,na.rm=TRUE)
[1] 1847.630 1401.609 1476.821 1469.865 0.000 1382.330 1504.983 1383.802
[9] 1431.881 1463.174
> rowVars(tmp5,na.rm=TRUE)
[1] 7705.80854 68.54568 53.39904 76.45945 NA 58.17965
[7] 76.04307 86.72649 58.54475 94.42662
> rowSd(tmp5,na.rm=TRUE)
[1] 87.782735 8.279232 7.307465 8.744109 NA 7.627559 8.720268
[8] 9.312706 7.651454 9.717336
> rowMax(tmp5,na.rm=TRUE)
[1] 464.06185 87.82239 86.90706 87.28831 NA 84.31931 92.64372
[8] 88.28482 87.11098 97.54408
> rowMin(tmp5,na.rm=TRUE)
[1] 59.86809 54.93617 62.56190 60.34213 NA 55.54634 59.26666 53.93708
[9] 59.83844 59.12080
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 113.84515 71.70986 73.52285 76.79960 70.87034 73.97824 71.95837
[8] 74.04933 71.87660 74.21197 71.53992 67.37457 NaN 71.21865
[15] 70.77507 73.46194 74.40718 72.33824 74.93928 63.34800
> colSums(tmp5,na.rm=TRUE)
[1] 1024.6063 645.3887 661.7057 691.1964 637.8331 665.8042 647.6253
[8] 666.4439 646.8894 667.9077 643.8592 606.3712 0.0000 640.9679
[15] 636.9756 661.1575 669.6646 651.0441 674.4535 570.1320
> colVars(tmp5,na.rm=TRUE)
[1] 17298.52149 64.36163 119.17803 92.80591 37.61493 103.76251
[7] 42.54233 59.58490 38.69043 116.41760 48.28809 33.53143
[13] NA 133.08084 28.50066 93.69219 40.04169 69.49269
[19] 58.78467 46.43186
> colSd(tmp5,na.rm=TRUE)
[1] 131.523844 8.022570 10.916869 9.633582 6.133101 10.186388
[7] 6.522448 7.719126 6.220163 10.789699 6.948964 5.790633
[13] NA 11.536067 5.338601 9.679473 6.327850 8.336228
[19] 7.667116 6.814093
> colMax(tmp5,na.rm=TRUE)
[1] 464.06185 81.58845 88.28482 97.54408 81.03897 92.09251 83.97702
[8] 86.31713 79.34677 96.45366 80.90016 77.50486 -Inf 92.64372
[15] 79.75514 87.11098 84.83747 84.39501 87.28831 72.53168
> colMin(tmp5,na.rm=TRUE)
[1] 59.83844 61.34556 58.27150 67.74011 61.68013 60.32313 60.60942 62.69280
[9] 63.77181 59.49477 59.26666 59.12080 Inf 56.82137 63.34598 61.08431
[17] 65.54605 58.26357 64.32271 54.93617
>
>
>
>
> 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] 134.8151 209.1590 150.8591 155.5094 251.5315 294.6004 151.3490 268.7429
[9] 182.7835 240.8826
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 134.8151 209.1590 150.8591 155.5094 251.5315 294.6004 151.3490 268.7429
[9] 182.7835 240.8826
>
>
>
> 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] 0.000000e+00 -1.136868e-13 -2.842171e-14 0.000000e+00 -5.684342e-14
[6] 0.000000e+00 -2.842171e-14 2.842171e-14 2.842171e-14 -1.421085e-14
[11] -8.526513e-14 0.000000e+00 -2.842171e-14 5.684342e-14 3.410605e-13
[16] 0.000000e+00 -8.526513e-14 5.684342e-14 -1.421085e-13 -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)
+ }
4 9
5 9
3 14
6 5
9 1
4 1
10 7
3 18
8 1
8 5
5 12
6 18
7 2
7 5
3 6
9 13
8 5
10 5
4 14
3 10
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] 1.986323
> Min(tmp)
[1] -2.104527
> mean(tmp)
[1] 0.0158031
> Sum(tmp)
[1] 1.58031
> Var(tmp)
[1] 0.9230231
>
> rowMeans(tmp)
[1] 0.0158031
> rowSums(tmp)
[1] 1.58031
> rowVars(tmp)
[1] 0.9230231
> rowSd(tmp)
[1] 0.9607409
> rowMax(tmp)
[1] 1.986323
> rowMin(tmp)
[1] -2.104527
>
> colMeans(tmp)
[1] 0.667446686 -0.833820963 -0.162215337 0.287385452 -0.104258000
[6] 0.231819391 0.603030412 -1.073179721 1.404863577 0.888274929
[11] -0.141086751 -1.471769346 -1.860363725 -1.235176532 1.271469233
[16] 0.194138969 1.804968490 0.533400601 -0.765748757 -0.903981352
[21] 0.914424128 -0.007769363 -0.006637702 -0.635286430 -0.187523559
[26] -0.898951298 -1.178013302 -0.027982379 1.158962732 -1.184736137
[31] 0.537178839 -0.995372081 1.501635551 -1.376428513 1.344117068
[36] -1.074845074 1.674582713 1.010607238 1.604370263 -0.021272731
[41] -1.497206762 1.486662588 0.026396820 -0.392623818 0.138330901
[46] 0.357720856 -0.142585487 -0.691577438 0.132263569 1.171480571
[51] -0.808007283 -0.449889751 1.204834390 0.444157418 0.467879230
[56] -0.039068341 1.986322516 -1.197226489 0.078023480 0.150426474
[61] -0.621089253 0.257837708 -0.720280974 -0.018221777 -0.869961401
[66] -1.027700961 0.293151452 0.556212591 -0.471880504 -1.002862164
[71] 0.851944635 1.595141241 0.477109674 -0.865592279 -0.900138839
[76] -0.015628449 0.702969845 0.792283182 -0.745138779 0.380734935
[81] 0.309344068 1.162823731 -0.330306386 -0.007719954 0.306633963
[86] -0.445856860 1.930680332 1.011869037 -0.526284461 0.597064849
[91] 0.509300299 -1.773064338 -1.848425997 -1.784583122 0.676763316
[96] 1.354250944 -0.511594975 -2.104527201 0.804977405 -0.312495110
> colSums(tmp)
[1] 0.667446686 -0.833820963 -0.162215337 0.287385452 -0.104258000
[6] 0.231819391 0.603030412 -1.073179721 1.404863577 0.888274929
[11] -0.141086751 -1.471769346 -1.860363725 -1.235176532 1.271469233
[16] 0.194138969 1.804968490 0.533400601 -0.765748757 -0.903981352
[21] 0.914424128 -0.007769363 -0.006637702 -0.635286430 -0.187523559
[26] -0.898951298 -1.178013302 -0.027982379 1.158962732 -1.184736137
[31] 0.537178839 -0.995372081 1.501635551 -1.376428513 1.344117068
[36] -1.074845074 1.674582713 1.010607238 1.604370263 -0.021272731
[41] -1.497206762 1.486662588 0.026396820 -0.392623818 0.138330901
[46] 0.357720856 -0.142585487 -0.691577438 0.132263569 1.171480571
[51] -0.808007283 -0.449889751 1.204834390 0.444157418 0.467879230
[56] -0.039068341 1.986322516 -1.197226489 0.078023480 0.150426474
[61] -0.621089253 0.257837708 -0.720280974 -0.018221777 -0.869961401
[66] -1.027700961 0.293151452 0.556212591 -0.471880504 -1.002862164
[71] 0.851944635 1.595141241 0.477109674 -0.865592279 -0.900138839
[76] -0.015628449 0.702969845 0.792283182 -0.745138779 0.380734935
[81] 0.309344068 1.162823731 -0.330306386 -0.007719954 0.306633963
[86] -0.445856860 1.930680332 1.011869037 -0.526284461 0.597064849
[91] 0.509300299 -1.773064338 -1.848425997 -1.784583122 0.676763316
[96] 1.354250944 -0.511594975 -2.104527201 0.804977405 -0.312495110
> 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] 0.667446686 -0.833820963 -0.162215337 0.287385452 -0.104258000
[6] 0.231819391 0.603030412 -1.073179721 1.404863577 0.888274929
[11] -0.141086751 -1.471769346 -1.860363725 -1.235176532 1.271469233
[16] 0.194138969 1.804968490 0.533400601 -0.765748757 -0.903981352
[21] 0.914424128 -0.007769363 -0.006637702 -0.635286430 -0.187523559
[26] -0.898951298 -1.178013302 -0.027982379 1.158962732 -1.184736137
[31] 0.537178839 -0.995372081 1.501635551 -1.376428513 1.344117068
[36] -1.074845074 1.674582713 1.010607238 1.604370263 -0.021272731
[41] -1.497206762 1.486662588 0.026396820 -0.392623818 0.138330901
[46] 0.357720856 -0.142585487 -0.691577438 0.132263569 1.171480571
[51] -0.808007283 -0.449889751 1.204834390 0.444157418 0.467879230
[56] -0.039068341 1.986322516 -1.197226489 0.078023480 0.150426474
[61] -0.621089253 0.257837708 -0.720280974 -0.018221777 -0.869961401
[66] -1.027700961 0.293151452 0.556212591 -0.471880504 -1.002862164
[71] 0.851944635 1.595141241 0.477109674 -0.865592279 -0.900138839
[76] -0.015628449 0.702969845 0.792283182 -0.745138779 0.380734935
[81] 0.309344068 1.162823731 -0.330306386 -0.007719954 0.306633963
[86] -0.445856860 1.930680332 1.011869037 -0.526284461 0.597064849
[91] 0.509300299 -1.773064338 -1.848425997 -1.784583122 0.676763316
[96] 1.354250944 -0.511594975 -2.104527201 0.804977405 -0.312495110
> colMin(tmp)
[1] 0.667446686 -0.833820963 -0.162215337 0.287385452 -0.104258000
[6] 0.231819391 0.603030412 -1.073179721 1.404863577 0.888274929
[11] -0.141086751 -1.471769346 -1.860363725 -1.235176532 1.271469233
[16] 0.194138969 1.804968490 0.533400601 -0.765748757 -0.903981352
[21] 0.914424128 -0.007769363 -0.006637702 -0.635286430 -0.187523559
[26] -0.898951298 -1.178013302 -0.027982379 1.158962732 -1.184736137
[31] 0.537178839 -0.995372081 1.501635551 -1.376428513 1.344117068
[36] -1.074845074 1.674582713 1.010607238 1.604370263 -0.021272731
[41] -1.497206762 1.486662588 0.026396820 -0.392623818 0.138330901
[46] 0.357720856 -0.142585487 -0.691577438 0.132263569 1.171480571
[51] -0.808007283 -0.449889751 1.204834390 0.444157418 0.467879230
[56] -0.039068341 1.986322516 -1.197226489 0.078023480 0.150426474
[61] -0.621089253 0.257837708 -0.720280974 -0.018221777 -0.869961401
[66] -1.027700961 0.293151452 0.556212591 -0.471880504 -1.002862164
[71] 0.851944635 1.595141241 0.477109674 -0.865592279 -0.900138839
[76] -0.015628449 0.702969845 0.792283182 -0.745138779 0.380734935
[81] 0.309344068 1.162823731 -0.330306386 -0.007719954 0.306633963
[86] -0.445856860 1.930680332 1.011869037 -0.526284461 0.597064849
[91] 0.509300299 -1.773064338 -1.848425997 -1.784583122 0.676763316
[96] 1.354250944 -0.511594975 -2.104527201 0.804977405 -0.312495110
> colMedians(tmp)
[1] 0.667446686 -0.833820963 -0.162215337 0.287385452 -0.104258000
[6] 0.231819391 0.603030412 -1.073179721 1.404863577 0.888274929
[11] -0.141086751 -1.471769346 -1.860363725 -1.235176532 1.271469233
[16] 0.194138969 1.804968490 0.533400601 -0.765748757 -0.903981352
[21] 0.914424128 -0.007769363 -0.006637702 -0.635286430 -0.187523559
[26] -0.898951298 -1.178013302 -0.027982379 1.158962732 -1.184736137
[31] 0.537178839 -0.995372081 1.501635551 -1.376428513 1.344117068
[36] -1.074845074 1.674582713 1.010607238 1.604370263 -0.021272731
[41] -1.497206762 1.486662588 0.026396820 -0.392623818 0.138330901
[46] 0.357720856 -0.142585487 -0.691577438 0.132263569 1.171480571
[51] -0.808007283 -0.449889751 1.204834390 0.444157418 0.467879230
[56] -0.039068341 1.986322516 -1.197226489 0.078023480 0.150426474
[61] -0.621089253 0.257837708 -0.720280974 -0.018221777 -0.869961401
[66] -1.027700961 0.293151452 0.556212591 -0.471880504 -1.002862164
[71] 0.851944635 1.595141241 0.477109674 -0.865592279 -0.900138839
[76] -0.015628449 0.702969845 0.792283182 -0.745138779 0.380734935
[81] 0.309344068 1.162823731 -0.330306386 -0.007719954 0.306633963
[86] -0.445856860 1.930680332 1.011869037 -0.526284461 0.597064849
[91] 0.509300299 -1.773064338 -1.848425997 -1.784583122 0.676763316
[96] 1.354250944 -0.511594975 -2.104527201 0.804977405 -0.312495110
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] 0.6674467 -0.833821 -0.1622153 0.2873855 -0.104258 0.2318194 0.6030304
[2,] 0.6674467 -0.833821 -0.1622153 0.2873855 -0.104258 0.2318194 0.6030304
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] -1.07318 1.404864 0.8882749 -0.1410868 -1.471769 -1.860364 -1.235177
[2,] -1.07318 1.404864 0.8882749 -0.1410868 -1.471769 -1.860364 -1.235177
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] 1.271469 0.194139 1.804968 0.5334006 -0.7657488 -0.9039814 0.9144241
[2,] 1.271469 0.194139 1.804968 0.5334006 -0.7657488 -0.9039814 0.9144241
[,22] [,23] [,24] [,25] [,26] [,27]
[1,] -0.007769363 -0.006637702 -0.6352864 -0.1875236 -0.8989513 -1.178013
[2,] -0.007769363 -0.006637702 -0.6352864 -0.1875236 -0.8989513 -1.178013
[,28] [,29] [,30] [,31] [,32] [,33] [,34]
[1,] -0.02798238 1.158963 -1.184736 0.5371788 -0.9953721 1.501636 -1.376429
[2,] -0.02798238 1.158963 -1.184736 0.5371788 -0.9953721 1.501636 -1.376429
[,35] [,36] [,37] [,38] [,39] [,40] [,41]
[1,] 1.344117 -1.074845 1.674583 1.010607 1.60437 -0.02127273 -1.497207
[2,] 1.344117 -1.074845 1.674583 1.010607 1.60437 -0.02127273 -1.497207
[,42] [,43] [,44] [,45] [,46] [,47] [,48]
[1,] 1.486663 0.02639682 -0.3926238 0.1383309 0.3577209 -0.1425855 -0.6915774
[2,] 1.486663 0.02639682 -0.3926238 0.1383309 0.3577209 -0.1425855 -0.6915774
[,49] [,50] [,51] [,52] [,53] [,54] [,55]
[1,] 0.1322636 1.171481 -0.8080073 -0.4498898 1.204834 0.4441574 0.4678792
[2,] 0.1322636 1.171481 -0.8080073 -0.4498898 1.204834 0.4441574 0.4678792
[,56] [,57] [,58] [,59] [,60] [,61] [,62]
[1,] -0.03906834 1.986323 -1.197226 0.07802348 0.1504265 -0.6210893 0.2578377
[2,] -0.03906834 1.986323 -1.197226 0.07802348 0.1504265 -0.6210893 0.2578377
[,63] [,64] [,65] [,66] [,67] [,68] [,69]
[1,] -0.720281 -0.01822178 -0.8699614 -1.027701 0.2931515 0.5562126 -0.4718805
[2,] -0.720281 -0.01822178 -0.8699614 -1.027701 0.2931515 0.5562126 -0.4718805
[,70] [,71] [,72] [,73] [,74] [,75] [,76]
[1,] -1.002862 0.8519446 1.595141 0.4771097 -0.8655923 -0.9001388 -0.01562845
[2,] -1.002862 0.8519446 1.595141 0.4771097 -0.8655923 -0.9001388 -0.01562845
[,77] [,78] [,79] [,80] [,81] [,82] [,83]
[1,] 0.7029698 0.7922832 -0.7451388 0.3807349 0.3093441 1.162824 -0.3303064
[2,] 0.7029698 0.7922832 -0.7451388 0.3807349 0.3093441 1.162824 -0.3303064
[,84] [,85] [,86] [,87] [,88] [,89] [,90]
[1,] -0.007719954 0.306634 -0.4458569 1.93068 1.011869 -0.5262845 0.5970648
[2,] -0.007719954 0.306634 -0.4458569 1.93068 1.011869 -0.5262845 0.5970648
[,91] [,92] [,93] [,94] [,95] [,96] [,97]
[1,] 0.5093003 -1.773064 -1.848426 -1.784583 0.6767633 1.354251 -0.511595
[2,] 0.5093003 -1.773064 -1.848426 -1.784583 0.6767633 1.354251 -0.511595
[,98] [,99] [,100]
[1,] -2.104527 0.8049774 -0.3124951
[2,] -2.104527 0.8049774 -0.3124951
>
>
> Max(tmp2)
[1] 2.33017
> Min(tmp2)
[1] -2.697696
> mean(tmp2)
[1] -0.03557292
> Sum(tmp2)
[1] -3.557292
> Var(tmp2)
[1] 0.9978821
>
> rowMeans(tmp2)
[1] 1.04789458 -0.65468975 0.40407194 1.23950712 -1.07167817 -1.48880128
[7] 0.75770253 0.37274631 -1.45286954 0.09849013 -0.99919471 -0.93724485
[13] -2.64141472 -0.37866975 -0.23939227 -2.69769634 -2.22828795 -0.02945385
[19] -0.01093166 0.35556378 -0.03348097 0.69191885 0.27146222 -0.54004920
[25] -0.06629116 -0.64376924 1.01200939 -0.22206146 0.66741468 0.36544247
[31] 0.64544169 1.06852627 -0.72853607 2.05247297 2.23237863 -1.70794673
[37] -0.22835198 -0.62385807 0.15507529 -0.45180154 -0.61803515 0.28114927
[43] 0.29268292 -1.34784843 1.25126071 2.10638309 -0.65459926 -0.19095162
[49] 0.24615736 0.76350006 1.10889635 -0.29012440 -1.51974986 -1.67044534
[55] 0.61943072 0.39240550 -1.35587430 0.33948938 0.05019003 -0.57647433
[61] 0.99583892 -1.40868033 0.50537412 0.16697812 -0.57671739 -0.15011578
[67] 0.06383613 2.33016965 1.70294872 0.85715103 -0.67990616 -0.06273280
[73] 0.68845817 1.45652536 -0.66917651 -0.02668724 -0.79350542 -0.47064279
[79] -1.20078540 -0.39966432 0.20284063 1.63077890 0.13902897 -0.67539607
[85] 0.94364358 0.30873165 -0.78263939 -0.25485071 1.17995562 -1.00560315
[91] -0.05105726 0.29713222 0.97639805 0.39735726 -0.75715575 -0.97917252
[97] -0.10592986 -0.58434001 1.41359537 -0.76836623
> rowSums(tmp2)
[1] 1.04789458 -0.65468975 0.40407194 1.23950712 -1.07167817 -1.48880128
[7] 0.75770253 0.37274631 -1.45286954 0.09849013 -0.99919471 -0.93724485
[13] -2.64141472 -0.37866975 -0.23939227 -2.69769634 -2.22828795 -0.02945385
[19] -0.01093166 0.35556378 -0.03348097 0.69191885 0.27146222 -0.54004920
[25] -0.06629116 -0.64376924 1.01200939 -0.22206146 0.66741468 0.36544247
[31] 0.64544169 1.06852627 -0.72853607 2.05247297 2.23237863 -1.70794673
[37] -0.22835198 -0.62385807 0.15507529 -0.45180154 -0.61803515 0.28114927
[43] 0.29268292 -1.34784843 1.25126071 2.10638309 -0.65459926 -0.19095162
[49] 0.24615736 0.76350006 1.10889635 -0.29012440 -1.51974986 -1.67044534
[55] 0.61943072 0.39240550 -1.35587430 0.33948938 0.05019003 -0.57647433
[61] 0.99583892 -1.40868033 0.50537412 0.16697812 -0.57671739 -0.15011578
[67] 0.06383613 2.33016965 1.70294872 0.85715103 -0.67990616 -0.06273280
[73] 0.68845817 1.45652536 -0.66917651 -0.02668724 -0.79350542 -0.47064279
[79] -1.20078540 -0.39966432 0.20284063 1.63077890 0.13902897 -0.67539607
[85] 0.94364358 0.30873165 -0.78263939 -0.25485071 1.17995562 -1.00560315
[91] -0.05105726 0.29713222 0.97639805 0.39735726 -0.75715575 -0.97917252
[97] -0.10592986 -0.58434001 1.41359537 -0.76836623
> 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] 1.04789458 -0.65468975 0.40407194 1.23950712 -1.07167817 -1.48880128
[7] 0.75770253 0.37274631 -1.45286954 0.09849013 -0.99919471 -0.93724485
[13] -2.64141472 -0.37866975 -0.23939227 -2.69769634 -2.22828795 -0.02945385
[19] -0.01093166 0.35556378 -0.03348097 0.69191885 0.27146222 -0.54004920
[25] -0.06629116 -0.64376924 1.01200939 -0.22206146 0.66741468 0.36544247
[31] 0.64544169 1.06852627 -0.72853607 2.05247297 2.23237863 -1.70794673
[37] -0.22835198 -0.62385807 0.15507529 -0.45180154 -0.61803515 0.28114927
[43] 0.29268292 -1.34784843 1.25126071 2.10638309 -0.65459926 -0.19095162
[49] 0.24615736 0.76350006 1.10889635 -0.29012440 -1.51974986 -1.67044534
[55] 0.61943072 0.39240550 -1.35587430 0.33948938 0.05019003 -0.57647433
[61] 0.99583892 -1.40868033 0.50537412 0.16697812 -0.57671739 -0.15011578
[67] 0.06383613 2.33016965 1.70294872 0.85715103 -0.67990616 -0.06273280
[73] 0.68845817 1.45652536 -0.66917651 -0.02668724 -0.79350542 -0.47064279
[79] -1.20078540 -0.39966432 0.20284063 1.63077890 0.13902897 -0.67539607
[85] 0.94364358 0.30873165 -0.78263939 -0.25485071 1.17995562 -1.00560315
[91] -0.05105726 0.29713222 0.97639805 0.39735726 -0.75715575 -0.97917252
[97] -0.10592986 -0.58434001 1.41359537 -0.76836623
> rowMin(tmp2)
[1] 1.04789458 -0.65468975 0.40407194 1.23950712 -1.07167817 -1.48880128
[7] 0.75770253 0.37274631 -1.45286954 0.09849013 -0.99919471 -0.93724485
[13] -2.64141472 -0.37866975 -0.23939227 -2.69769634 -2.22828795 -0.02945385
[19] -0.01093166 0.35556378 -0.03348097 0.69191885 0.27146222 -0.54004920
[25] -0.06629116 -0.64376924 1.01200939 -0.22206146 0.66741468 0.36544247
[31] 0.64544169 1.06852627 -0.72853607 2.05247297 2.23237863 -1.70794673
[37] -0.22835198 -0.62385807 0.15507529 -0.45180154 -0.61803515 0.28114927
[43] 0.29268292 -1.34784843 1.25126071 2.10638309 -0.65459926 -0.19095162
[49] 0.24615736 0.76350006 1.10889635 -0.29012440 -1.51974986 -1.67044534
[55] 0.61943072 0.39240550 -1.35587430 0.33948938 0.05019003 -0.57647433
[61] 0.99583892 -1.40868033 0.50537412 0.16697812 -0.57671739 -0.15011578
[67] 0.06383613 2.33016965 1.70294872 0.85715103 -0.67990616 -0.06273280
[73] 0.68845817 1.45652536 -0.66917651 -0.02668724 -0.79350542 -0.47064279
[79] -1.20078540 -0.39966432 0.20284063 1.63077890 0.13902897 -0.67539607
[85] 0.94364358 0.30873165 -0.78263939 -0.25485071 1.17995562 -1.00560315
[91] -0.05105726 0.29713222 0.97639805 0.39735726 -0.75715575 -0.97917252
[97] -0.10592986 -0.58434001 1.41359537 -0.76836623
>
> colMeans(tmp2)
[1] -0.03557292
> colSums(tmp2)
[1] -3.557292
> colVars(tmp2)
[1] 0.9978821
> colSd(tmp2)
[1] 0.9989405
> colMax(tmp2)
[1] 2.33017
> colMin(tmp2)
[1] -2.697696
> colMedians(tmp2)
[1] -0.03146741
> colRanges(tmp2)
[,1]
[1,] -2.697696
[2,] 2.330170
>
> 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] -1.0260288 1.7619182 1.3831045 -1.3252739 6.1714726 -0.7241302
[7] 4.9735458 3.1408993 2.4957219 -1.8386120
> colApply(tmp,quantile)[,1]
[,1]
[1,] -2.6391733
[2,] -0.6571755
[3,] 0.2655257
[4,] 0.7181117
[5,] 1.4473757
>
> rowApply(tmp,sum)
[1] -0.6612802 8.2513096 5.3309712 4.5039977 -1.2213637 -0.1601999
[7] -2.5048457 3.4784124 -3.7411844 1.7368004
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 7 6 5 10 1 2 6 6 1 9
[2,] 9 3 4 9 4 1 3 7 8 7
[3,] 3 5 1 7 10 4 5 5 9 4
[4,] 2 8 8 5 2 9 9 1 3 2
[5,] 10 10 10 4 8 8 7 4 5 5
[6,] 5 2 2 2 5 7 1 10 4 3
[7,] 4 9 6 6 6 6 10 9 6 8
[8,] 1 4 3 3 7 10 2 8 7 10
[9,] 8 1 9 1 9 5 4 3 10 6
[10,] 6 7 7 8 3 3 8 2 2 1
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] -1.0149528 1.8029205 3.0859123 -3.0773366 1.4901060 -2.1964020
[7] 4.7332086 -1.3718094 -0.1687066 0.1148413 2.7869163 3.7902698
[13] 0.9559801 -4.1676785 -3.5881771 -2.0011257 -0.5399208 -0.5567143
[19] -2.7425476 1.7894760
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.34074243
[2,] -0.55292151
[3,] -0.17895352
[4,] 0.08244471
[5,] 0.97521996
>
> rowApply(tmp,sum)
[1] -3.47189808 -8.27303483 5.82963537 5.09625414 -0.05669709
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 11 3 13 4 10
[2,] 3 11 18 14 16
[3,] 8 20 20 7 11
[4,] 1 6 5 13 18
[5,] 19 5 17 16 2
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] -0.17895352 -1.1062774 -0.5635014 -2.6048529 1.329898 -0.90189932
[2,] -1.34074243 -0.5594782 1.2120780 -1.1806983 -1.182773 0.04660761
[3,] 0.97521996 2.2403978 2.4354893 -0.9377835 1.650165 -0.11102738
[4,] -0.55292151 0.6914845 -0.1217013 0.5706255 0.941808 -1.17509257
[5,] 0.08244471 0.5367939 0.1235477 1.0753725 -1.248992 -0.05499033
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] 0.7773300 -0.6684106 1.2223983 1.3649943 1.3105002 0.01561542
[2,] 1.0814655 0.2725471 0.7165639 -0.4144340 -1.1633745 0.60749191
[3,] 0.8162602 -1.9630444 -2.3300565 -0.4384646 0.2580731 1.17877470
[4,] 1.6085190 0.1596368 1.2971905 0.4708754 2.0458344 -0.22682248
[5,] 0.4496339 0.8274617 -1.0748028 -0.8681298 0.3358830 2.21521025
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] -0.6431787 -0.1130085 -1.4631160 -1.03025305 0.3384133 -0.4389081
[2,] -0.7032704 -1.5430062 0.3829218 -0.99916652 0.6241466 -1.7187551
[3,] 1.4321915 -0.1421014 -1.4124356 0.12511613 -1.0744152 2.4268213
[4,] 2.2630173 -2.5124812 0.1510615 -0.05682938 0.7173291 -1.1464656
[5,] -1.3927796 0.1429188 -1.2466089 -0.03999291 -1.1453947 0.3205933
[,19] [,20]
[1,] -0.3109882 0.1922997
[2,] -1.1543027 -1.2568558
[3,] -0.3350303 1.0354849
[4,] -0.5467232 0.5179095
[5,] -0.3955032 1.3006377
>
>
> is.BufferedMatrix(tmp)
[1] TRUE
>
> as.BufferedMatrix(as.matrix(tmp))
BufferedMatrix object
Matrix size: 5 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.24-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-3.24-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 654 bytes.
Disk usage : 200 bytes.
> subBufferedMatrix(tmp,,5:8)
BufferedMatrix object
Matrix size: 5 4
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.24-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-3.24-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 0.4929049 -1.365872 -0.1552196 1.993272 -1.545355 0.07763671 0.2895444
col8 col9 col10 col11 col12 col13 col14
row1 1.096439 -0.1258611 -1.627854 -0.6395428 -0.06766479 -1.281332 1.008315
col15 col16 col17 col18 col19 col20
row1 -0.1437149 -0.8270898 0.2362822 -0.2552992 1.296187 1.030836
> tmp[,"col10"]
col10
row1 -1.62785437
row2 -0.06517092
row3 0.34041463
row4 -0.67104036
row5 1.25301915
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7
row1 0.4929049 -1.3658717 -0.1552196 1.9932725 -1.545355 0.07763671 0.2895444
row5 -1.2102833 -0.4776717 0.9493295 0.7622973 -1.247766 -0.73786377 1.0235094
col8 col9 col10 col11 col12 col13 col14
row1 1.0964391 -0.1258611 -1.627854 -0.6395428 -0.06766479 -1.2813321 1.008315
row5 0.3238902 0.3050834 1.253019 -1.5446963 0.35890934 0.6520728 1.530176
col15 col16 col17 col18 col19 col20
row1 -0.1437149 -0.8270898 0.23628217 -0.2552992 1.296187 1.0308356
row5 0.9509466 0.8617189 0.03748593 0.1570873 -1.773582 -0.5640749
> tmp[,c("col6","col20")]
col6 col20
row1 0.07763671 1.0308356
row2 -0.54398265 -1.1428218
row3 -0.53757424 0.2726402
row4 -0.45458763 0.3300025
row5 -0.73786377 -0.5640749
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 0.07763671 1.0308356
row5 -0.73786377 -0.5640749
>
>
>
>
> 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 47.02654 51.49322 50.31225 50.65464 50.20101 104.8982 50.85129 50.41846
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.11184 51.13752 50.03549 50.85178 48.48044 49.9712 50.80162 50.0424
col17 col18 col19 col20
row1 48.93988 51.32826 50.98834 104.0888
> tmp[,"col10"]
col10
row1 51.13752
row2 29.97329
row3 30.53746
row4 30.73307
row5 47.10911
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 47.02654 51.49322 50.31225 50.65464 50.20101 104.8982 50.85129 50.41846
row5 50.20890 49.31197 49.59799 49.21201 51.44663 105.0494 49.91266 50.14624
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.11184 51.13752 50.03549 50.85178 48.48044 49.97120 50.80162 50.04240
row5 50.77253 47.10911 49.79405 50.75373 50.05071 49.96934 50.00067 48.87181
col17 col18 col19 col20
row1 48.93988 51.32826 50.98834 104.0888
row5 50.68218 48.28584 50.29472 105.8172
> tmp[,c("col6","col20")]
col6 col20
row1 104.89820 104.08883
row2 75.15908 74.04032
row3 74.11508 77.38218
row4 74.69512 75.33830
row5 105.04944 105.81715
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 104.8982 104.0888
row5 105.0494 105.8172
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 104.8982 104.0888
row5 105.0494 105.8172
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] -0.2141157
[2,] -0.1709220
[3,] 1.5150324
[4,] 0.6821335
[5,] -0.5518042
> tmp[,c("col17","col7")]
col17 col7
[1,] 1.68658475 -0.6274672
[2,] -0.01963705 1.8884057
[3,] -0.03780920 -0.7598625
[4,] -0.91754062 -0.7487457
[5,] -1.70736421 0.6961646
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] -0.49657127 0.5789113
[2,] -0.35639186 0.4963777
[3,] 0.89548866 -0.8948747
[4,] -0.07114871 1.6546681
[5,] -0.33874673 -0.6122398
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] -0.4965713
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] -0.4965713
[2,] -0.3563919
>
>
>
> 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 0.1438631 0.4646706 0.3886431 0.3868157 0.4535993 -0.9813693 0.5613206
row1 -1.3247497 -0.9415906 1.0146202 -1.9761240 0.3757632 1.4136070 1.0950776
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row3 -0.7440266 -1.303818 2.162646 1.3124121 -0.1620262 1.0213054 0.3817752
row1 -1.0747730 1.564451 -0.430335 -0.7395312 1.0480962 -0.7122494 -0.3334614
[,15] [,16] [,17] [,18] [,19] [,20]
row3 -0.8022407 0.1702645 -0.08133186 -0.6087134 1.7433053 -1.3142238
row1 -0.3350551 -1.0649713 -1.66564383 -0.3369962 -0.8962095 0.9301057
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 -0.7651807 0.1044107 1.097933 -0.007405627 0.7370765 0.7767338 -0.5406701
[,8] [,9] [,10]
row2 -0.2914021 0.1347854 0.00544691
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 -0.1264669 0.001602059 -1.944228 1.240337 0.2197286 0.8854618 -3.461772
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 1.262417 0.1636256 0.4137707 -0.2160465 0.2655641 -0.47288 -0.502129
[,15] [,16] [,17] [,18] [,19] [,20]
row5 0.7549625 0.3346734 -0.2262394 0.3328439 0.532477 1.55585
>
>
> 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: 0x648bc9be69b0>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests/BM1912c67f985385"
[2] "/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests/BM1912c6b017cf2"
[3] "/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests/BM1912c6c1dbfb5"
[4] "/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests/BM1912c63ab821c3"
[5] "/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests/BM1912c628de927c"
[6] "/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests/BM1912c6632e2c53"
[7] "/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests/BM1912c62f52e364"
[8] "/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests/BM1912c661bd9eae"
[9] "/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests/BM1912c6cd57788"
[10] "/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests/BM1912c64986dd42"
[11] "/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests/BM1912c61da56338"
[12] "/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests/BM1912c61fb33df"
[13] "/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests/BM1912c641abe1de"
[14] "/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests/BM1912c64ca06a29"
[15] "/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests/BM1912c61c05a2fa"
>
>
> ### 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: 0x648bca42b540>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x648bca42b540>
Warning message:
In dir.create(new.directory) :
'/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x648bca42b540>
> rowMedians(tmp)
[1] 0.300651109 0.115186572 -0.470882153 0.154098067 0.202686097
[6] -0.594057797 -0.391761336 0.039560386 -0.112956699 0.046204473
[11] 0.391788219 -0.259791888 0.172482845 -0.140978781 0.071677120
[16] -0.508202734 -0.042766468 0.040489705 -0.049145123 -0.156167340
[21] 0.621393484 -0.105625018 -0.082560185 -0.051965250 0.379349989
[26] 0.341180207 0.332671999 0.007610253 0.635023773 0.165239058
[31] 0.291263277 0.592515636 -0.386726573 0.296843443 0.400639199
[36] -0.066378050 -0.459711346 0.361297289 0.136278303 -0.311179313
[41] 0.113591517 -0.759893796 -0.045369418 0.493016756 -0.370395716
[46] -0.280398036 0.117109241 0.310231431 0.600631551 0.060196780
[51] 0.456123546 -0.202590113 0.326209797 0.378434421 0.001571912
[56] 0.036972174 -0.208769487 0.159695515 0.022389622 -0.224819944
[61] 0.085475247 -0.026861700 -0.020142621 -0.010808822 0.011992740
[66] -0.488783173 -0.127400290 -0.267314036 -0.107520753 0.229692514
[71] 0.567304060 0.115224604 -0.172277406 0.074264263 -0.151333336
[76] 0.387951508 -0.251748824 -0.085990738 0.204999146 -0.443145944
[81] 0.172157594 -0.580285549 0.161077706 0.436197377 0.097317977
[86] 0.376784174 0.353451094 -0.159238574 -0.120294802 -0.016592438
[91] 0.039315775 0.097577804 -0.119057719 -0.012225801 0.259675353
[96] 0.211309865 -0.276731615 0.260655935 0.127152577 -0.280020292
[101] 0.047438594 -0.553940034 -0.162861221 0.100933581 0.078931713
[106] -0.107470339 -0.292866112 -0.087399540 0.060410950 0.209259267
[111] 0.478023492 0.049273113 -0.236185516 -0.135912649 0.233894914
[116] 0.458417052 -0.622093267 0.497742561 0.369324105 0.427496452
[121] 0.325745938 -0.339989424 0.295542326 -0.013199720 0.222062003
[126] -0.424882747 0.254334894 0.062377879 -0.199712426 -0.747957116
[131] 0.152270154 0.424301338 0.034028052 0.064372382 -0.047706212
[136] -0.107159026 -0.111552325 -0.023006370 0.121889595 -0.037481457
[141] -0.327960980 -0.216977605 -0.311307623 -0.675166728 0.297058345
[146] 0.089783600 -0.516488265 -0.125562548 0.136707871 -0.199869137
[151] 0.510662673 -0.236628222 0.052151469 -0.041824666 0.389656665
[156] -0.396144728 0.205580385 0.099205109 -0.415459797 -0.460605428
[161] -0.466640871 -0.090320235 0.786170072 -0.099670628 0.511066306
[166] 0.023504992 0.605059280 0.398403780 0.436193908 -0.385544082
[171] -0.493248559 -0.464154637 0.657068686 0.069558122 0.285467421
[176] 0.607839019 0.381432400 0.547656619 -0.202923889 0.136959356
[181] -0.180303582 0.480268046 0.243428376 0.576912328 -0.195405483
[186] 0.122362574 -0.341101335 -0.184175063 -0.827538997 -0.203791068
[191] -0.433510451 0.081014841 -0.564095222 0.708573886 -0.195547109
[196] 0.401009952 0.142479999 -0.171169482 0.120947815 -0.620498696
[201] 0.011412750 -0.503918108 0.384014069 0.234253087 -0.484972271
[206] -0.694031425 -0.368922240 -0.191125145 0.199247901 0.095504947
[211] -0.571846598 0.193268699 0.472373282 0.185070305 -0.137576469
[216] -0.334619475 -0.229044102 -0.446864247 -0.117286362 0.288188289
[221] 0.065705732 0.349432228 0.102008990 -0.168618764 -0.034553959
[226] -0.176477984 -0.034197409 -0.251267810 0.642156707 0.014486824
>
> proc.time()
user system elapsed
1.274 0.721 1.984
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
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: 0x59c697411520>
> .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: 0x59c697411520>
> .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: 0x59c697411520>
> .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: 0x59c697411520>
> 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: 0x59c696fbaf60>
> .Call("R_bm_AddColumn",P)
<pointer: 0x59c696fbaf60>
> .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: 0x59c696fbaf60>
> .Call("R_bm_AddColumn",P)
<pointer: 0x59c696fbaf60>
> .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: 0x59c696fbaf60>
> 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: 0x59c697b64b40>
> .Call("R_bm_AddColumn",P)
<pointer: 0x59c697b64b40>
> .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: 0x59c697b64b40>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x59c697b64b40>
> .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: 0x59c697b64b40>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x59c697b64b40>
> .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: 0x59c697b64b40>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x59c697b64b40>
> .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: 0x59c697b64b40>
> 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: 0x59c697ba1bc0>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x59c697ba1bc0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x59c697ba1bc0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x59c697ba1bc0>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile19142560911644" "BufferedMatrixFile1914256ef5842b"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile19142560911644" "BufferedMatrixFile1914256ef5842b"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x59c698f29de0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x59c698f29de0>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x59c698f29de0>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x59c698f29de0>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x59c698f29de0>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x59c698f29de0>
> .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: 0x59c696c5ff80>
> .Call("R_bm_AddColumn",P)
<pointer: 0x59c696c5ff80>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x59c696c5ff80>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x59c696c5ff80>
> 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: 0x59c697bfa690>
> .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: 0x59c697bfa690>
> rm(P)
>
> proc.time()
user system elapsed
0.259 0.048 0.296
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
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.
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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
0.255 0.041 0.285