Ben Bolstad
| Snapshot Date: 2026-01-26 13:45 -0500 (Mon, 26 Jan 2026) |
| git_url: https://git.bioconductor.org/packages/BufferedMatrix |
| git_branch: RELEASE_3_22 |
| git_last_commit: d2ce144 |
| git_last_commit_date: 2025-10-29 09:58:55 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-01-29 11:58 -0500 (Thu, 29 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4886 |
| 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 257/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BufferedMatrix 1.74.0 (landing page) Ben Bolstad
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the BufferedMatrix package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BufferedMatrix.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BufferedMatrix |
| Version: 1.74.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BufferedMatrix_1.74.0.tar.gz |
| StartedAt: 2026-01-26 21:50:33 -0500 (Mon, 26 Jan 2026) |
| EndedAt: 2026-01-26 21:50:57 -0500 (Mon, 26 Jan 2026) |
| EllapsedTime: 24.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BufferedMatrix_1.74.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘BufferedMatrix/DESCRIPTION’ ... OK
* this is package ‘BufferedMatrix’ version ‘1.74.0’
* 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) 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 ... NOTE
Note: information on .o files is not available
* 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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/00check.log’
for details.
BufferedMatrix.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL BufferedMatrix
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘BufferedMatrix’ ...
** this is package ‘BufferedMatrix’ version ‘1.74.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-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-3.22-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-3.22-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-3.22-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-3.22-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-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 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
0.273 0.035 0.298
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 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-3.22-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 478284 25.6 1046725 56 639600 34.2
Vcells 884773 6.8 8388608 64 2081613 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] "Mon Jan 26 21:50:48 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] "Mon Jan 26 21:50:48 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: 0x62bb5877f370>
>
>
>
> 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] "Mon Jan 26 21:50:48 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] "Mon Jan 26 21:50:48 2026"
>
> ColMode(tmp2)
<pointer: 0x62bb5877f370>
>
>
>
> ### 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,] 99.9538352 -0.4567952 0.3509548 -0.041424261
[2,] -0.1416446 -0.2740555 -0.3377433 0.341700291
[3,] 1.1156685 -0.6220650 0.6912165 0.004198621
[4,] 0.2232852 -0.6276653 0.2218687 -0.467053211
> ewApply(tmp5,abs)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.22-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,] 99.9538352 0.4567952 0.3509548 0.041424261
[2,] 0.1416446 0.2740555 0.3377433 0.341700291
[3,] 1.1156685 0.6220650 0.6912165 0.004198621
[4,] 0.2232852 0.6276653 0.2218687 0.467053211
> ewApply(tmp5,sqrt)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.22-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,] 9.9976915 0.6758663 0.5924144 0.20352951
[2,] 0.3763570 0.5235031 0.5811569 0.58455136
[3,] 1.0562521 0.7887110 0.8313943 0.06479677
[4,] 0.4725306 0.7922533 0.4710294 0.68341291
>
> 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-3.22-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,] 224.93075 32.21546 31.27510 27.07672
[2,] 28.90521 30.50909 31.14931 31.18721
[3,] 36.67819 33.50917 34.00516 25.65217
[4,] 29.94859 33.55020 29.93216 32.30118
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x62bb5977b9b0>
> exp(tmp5)
<pointer: 0x62bb5977b9b0>
> log(tmp5,2)
<pointer: 0x62bb5977b9b0>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 468.1639
> Min(tmp5)
[1] 52.88252
> mean(tmp5)
[1] 72.97714
> Sum(tmp5)
[1] 14595.43
> Var(tmp5)
[1] 853.8675
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 90.55054 68.70366 71.20492 72.31971 72.51058 70.02056 71.66249 72.59178
[9] 70.50184 69.70534
> rowSums(tmp5)
[1] 1811.011 1374.073 1424.098 1446.394 1450.212 1400.411 1433.250 1451.836
[9] 1410.037 1394.107
> rowVars(tmp5)
[1] 7967.63122 55.55789 77.93265 89.21011 91.26820 94.01746
[7] 49.43169 40.09816 72.26077 28.54385
> rowSd(tmp5)
[1] 89.261589 7.453716 8.827947 9.445110 9.553439 9.696260 7.030768
[8] 6.332311 8.500633 5.342644
> rowMax(tmp5)
[1] 468.16389 79.92320 86.52787 87.33022 84.27401 90.87941 87.02127
[8] 83.46924 93.86397 80.82975
> rowMin(tmp5)
[1] 56.35664 58.09642 53.39162 54.58877 52.88252 54.51867 58.29938 57.20933
[9] 56.04561 57.07890
>
> colMeans(tmp5)
[1] 110.28858 68.48559 68.51897 66.61844 70.51119 71.86435 68.09040
[8] 72.91823 76.25206 70.48648 71.71902 73.22023 69.53258 75.89945
[15] 69.83974 67.52595 74.00376 72.76959 69.23121 71.76697
> colSums(tmp5)
[1] 1102.8858 684.8559 685.1897 666.1844 705.1119 718.6435 680.9040
[8] 729.1823 762.5206 704.8648 717.1902 732.2023 695.3258 758.9945
[15] 698.3974 675.2595 740.0376 727.6959 692.3121 717.6697
> colVars(tmp5)
[1] 15864.97903 29.43033 62.23406 82.77787 53.06728 19.80862
[7] 35.60005 55.53965 81.14199 74.36549 43.63131 30.07885
[13] 95.77968 33.21948 109.89453 85.34145 73.02499 76.01010
[19] 94.38877 103.02846
> colSd(tmp5)
[1] 125.956258 5.424973 7.888857 9.098234 7.284729 4.450687
[7] 5.966577 7.452493 9.007885 8.623543 6.605400 5.484419
[13] 9.786709 5.763635 10.483059 9.238044 8.545466 8.718377
[19] 9.715388 10.150294
> colMax(tmp5)
[1] 468.16389 81.03788 81.99948 79.31511 81.29157 80.26405 78.32867
[8] 84.22746 93.86397 84.04273 86.52787 84.87307 84.19145 83.46924
[15] 87.33022 83.05542 90.87941 84.27401 83.59401 87.02127
> colMin(tmp5)
[1] 60.16242 61.06477 59.14014 53.39162 58.72779 66.56657 61.28288 62.55441
[9] 59.25391 57.95206 61.64321 66.97292 54.51867 69.04363 56.31358 56.40192
[17] 62.47628 54.58877 52.88252 57.20933
>
>
> ### 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] 90.55054 68.70366 NA 72.31971 72.51058 70.02056 71.66249 72.59178
[9] 70.50184 69.70534
> rowSums(tmp5)
[1] 1811.011 1374.073 NA 1446.394 1450.212 1400.411 1433.250 1451.836
[9] 1410.037 1394.107
> rowVars(tmp5)
[1] 7967.63122 55.55789 80.33647 89.21011 91.26820 94.01746
[7] 49.43169 40.09816 72.26077 28.54385
> rowSd(tmp5)
[1] 89.261589 7.453716 8.963062 9.445110 9.553439 9.696260 7.030768
[8] 6.332311 8.500633 5.342644
> rowMax(tmp5)
[1] 468.16389 79.92320 NA 87.33022 84.27401 90.87941 87.02127
[8] 83.46924 93.86397 80.82975
> rowMin(tmp5)
[1] 56.35664 58.09642 NA 54.58877 52.88252 54.51867 58.29938 57.20933
[9] 56.04561 57.07890
>
> colMeans(tmp5)
[1] 110.28858 68.48559 68.51897 66.61844 70.51119 71.86435 NA
[8] 72.91823 76.25206 70.48648 71.71902 73.22023 69.53258 75.89945
[15] 69.83974 67.52595 74.00376 72.76959 69.23121 71.76697
> colSums(tmp5)
[1] 1102.8858 684.8559 685.1897 666.1844 705.1119 718.6435 NA
[8] 729.1823 762.5206 704.8648 717.1902 732.2023 695.3258 758.9945
[15] 698.3974 675.2595 740.0376 727.6959 692.3121 717.6697
> colVars(tmp5)
[1] 15864.97903 29.43033 62.23406 82.77787 53.06728 19.80862
[7] NA 55.53965 81.14199 74.36549 43.63131 30.07885
[13] 95.77968 33.21948 109.89453 85.34145 73.02499 76.01010
[19] 94.38877 103.02846
> colSd(tmp5)
[1] 125.956258 5.424973 7.888857 9.098234 7.284729 4.450687
[7] NA 7.452493 9.007885 8.623543 6.605400 5.484419
[13] 9.786709 5.763635 10.483059 9.238044 8.545466 8.718377
[19] 9.715388 10.150294
> colMax(tmp5)
[1] 468.16389 81.03788 81.99948 79.31511 81.29157 80.26405 NA
[8] 84.22746 93.86397 84.04273 86.52787 84.87307 84.19145 83.46924
[15] 87.33022 83.05542 90.87941 84.27401 83.59401 87.02127
> colMin(tmp5)
[1] 60.16242 61.06477 59.14014 53.39162 58.72779 66.56657 NA 62.55441
[9] 59.25391 57.95206 61.64321 66.97292 54.51867 69.04363 56.31358 56.40192
[17] 62.47628 54.58877 52.88252 57.20933
>
> Max(tmp5,na.rm=TRUE)
[1] 468.1639
> Min(tmp5,na.rm=TRUE)
[1] 52.88252
> mean(tmp5,na.rm=TRUE)
[1] 73.01488
> Sum(tmp5,na.rm=TRUE)
[1] 14529.96
> Var(tmp5,na.rm=TRUE)
[1] 857.8937
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 90.55054 68.70366 71.50694 72.31971 72.51058 70.02056 71.66249 72.59178
[9] 70.50184 69.70534
> rowSums(tmp5,na.rm=TRUE)
[1] 1811.011 1374.073 1358.632 1446.394 1450.212 1400.411 1433.250 1451.836
[9] 1410.037 1394.107
> rowVars(tmp5,na.rm=TRUE)
[1] 7967.63122 55.55789 80.33647 89.21011 91.26820 94.01746
[7] 49.43169 40.09816 72.26077 28.54385
> rowSd(tmp5,na.rm=TRUE)
[1] 89.261589 7.453716 8.963062 9.445110 9.553439 9.696260 7.030768
[8] 6.332311 8.500633 5.342644
> rowMax(tmp5,na.rm=TRUE)
[1] 468.16389 79.92320 86.52787 87.33022 84.27401 90.87941 87.02127
[8] 83.46924 93.86397 80.82975
> rowMin(tmp5,na.rm=TRUE)
[1] 56.35664 58.09642 53.39162 54.58877 52.88252 54.51867 58.29938 57.20933
[9] 56.04561 57.07890
>
> colMeans(tmp5,na.rm=TRUE)
[1] 110.28858 68.48559 68.51897 66.61844 70.51119 71.86435 68.38196
[8] 72.91823 76.25206 70.48648 71.71902 73.22023 69.53258 75.89945
[15] 69.83974 67.52595 74.00376 72.76959 69.23121 71.76697
> colSums(tmp5,na.rm=TRUE)
[1] 1102.8858 684.8559 685.1897 666.1844 705.1119 718.6435 615.4376
[8] 729.1823 762.5206 704.8648 717.1902 732.2023 695.3258 758.9945
[15] 698.3974 675.2595 740.0376 727.6959 692.3121 717.6697
> colVars(tmp5,na.rm=TRUE)
[1] 15864.97903 29.43033 62.23406 82.77787 53.06728 19.80862
[7] 39.09374 55.53965 81.14199 74.36549 43.63131 30.07885
[13] 95.77968 33.21948 109.89453 85.34145 73.02499 76.01010
[19] 94.38877 103.02846
> colSd(tmp5,na.rm=TRUE)
[1] 125.956258 5.424973 7.888857 9.098234 7.284729 4.450687
[7] 6.252499 7.452493 9.007885 8.623543 6.605400 5.484419
[13] 9.786709 5.763635 10.483059 9.238044 8.545466 8.718377
[19] 9.715388 10.150294
> colMax(tmp5,na.rm=TRUE)
[1] 468.16389 81.03788 81.99948 79.31511 81.29157 80.26405 78.32867
[8] 84.22746 93.86397 84.04273 86.52787 84.87307 84.19145 83.46924
[15] 87.33022 83.05542 90.87941 84.27401 83.59401 87.02127
> colMin(tmp5,na.rm=TRUE)
[1] 60.16242 61.06477 59.14014 53.39162 58.72779 66.56657 61.28288 62.55441
[9] 59.25391 57.95206 61.64321 66.97292 54.51867 69.04363 56.31358 56.40192
[17] 62.47628 54.58877 52.88252 57.20933
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 90.55054 68.70366 NaN 72.31971 72.51058 70.02056 71.66249 72.59178
[9] 70.50184 69.70534
> rowSums(tmp5,na.rm=TRUE)
[1] 1811.011 1374.073 0.000 1446.394 1450.212 1400.411 1433.250 1451.836
[9] 1410.037 1394.107
> rowVars(tmp5,na.rm=TRUE)
[1] 7967.63122 55.55789 NA 89.21011 91.26820 94.01746
[7] 49.43169 40.09816 72.26077 28.54385
> rowSd(tmp5,na.rm=TRUE)
[1] 89.261589 7.453716 NA 9.445110 9.553439 9.696260 7.030768
[8] 6.332311 8.500633 5.342644
> rowMax(tmp5,na.rm=TRUE)
[1] 468.16389 79.92320 NA 87.33022 84.27401 90.87941 87.02127
[8] 83.46924 93.86397 80.82975
> rowMin(tmp5,na.rm=TRUE)
[1] 56.35664 58.09642 NA 54.58877 52.88252 54.51867 58.29938 57.20933
[9] 56.04561 57.07890
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 114.06055 68.34566 68.26804 68.08809 71.82046 72.37795 NaN
[8] 71.66165 76.19852 71.56084 70.07359 73.50168 68.88701 75.12024
[15] 70.84412 66.71498 73.45920 73.17893 69.60199 71.33562
> colSums(tmp5,na.rm=TRUE)
[1] 1026.5449 615.1110 614.4124 612.7928 646.3841 651.4016 0.0000
[8] 644.9548 685.7867 644.0475 630.6624 661.5151 619.9831 676.0822
[15] 637.5971 600.4348 661.1328 658.6104 626.4179 642.0206
> colVars(tmp5,na.rm=TRUE)
[1] 17688.03914 32.88884 69.30498 68.82667 40.41617 19.31715
[7] NA 44.71838 91.25249 70.67594 18.62660 32.94756
[13] 103.06355 30.54131 112.28254 88.61031 78.81691 83.62627
[19] 104.64075 113.81380
> colSd(tmp5,na.rm=TRUE)
[1] 132.996388 5.734879 8.324962 8.296184 6.357371 4.395128
[7] NA 6.687180 9.552617 8.406899 4.315855 5.739997
[13] 10.152022 5.526419 10.596346 9.413305 8.877889 9.144740
[19] 10.229406 10.668355
> colMax(tmp5,na.rm=TRUE)
[1] 468.16389 81.03788 81.99948 79.31511 81.29157 80.26405 -Inf
[8] 80.99855 93.86397 84.04273 75.45366 84.87307 84.19145 83.46924
[15] 87.33022 83.05542 90.87941 84.27401 83.59401 87.02127
> colMin(tmp5,na.rm=TRUE)
[1] 60.16242 61.06477 59.14014 54.99810 59.19033 66.56657 Inf 62.55441
[9] 59.25391 57.95206 61.64321 66.97292 54.51867 69.04363 56.31358 56.40192
[17] 62.47628 54.58877 52.88252 57.20933
>
>
>
>
> 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] 199.8166 220.6308 212.1889 288.8998 265.7832 192.1311 241.9523 127.2624
[9] 170.3857 246.1525
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 199.8166 220.6308 212.1889 288.8998 265.7832 192.1311 241.9523 127.2624
[9] 170.3857 246.1525
>
>
>
> copymatrix <- matrix(rnorm(200,150,15),10,20)
>
> tmp5[1:10,1:20] <- copymatrix
> which.row <- 1
> which.col <- 3
> cat(which.row," ",which.col,"\n")
1 3
> tmp5[which.row,which.col] <- NA
> copymatrix[which.row,which.col] <- NA
>
> colVars(tmp5,na.rm=TRUE)-apply(copymatrix,2,var,na.rm=TRUE)
[1] -5.684342e-14 -2.842171e-14 -1.136868e-13 9.947598e-14 2.273737e-13
[6] 1.705303e-13 1.136868e-13 -1.421085e-13 1.705303e-13 -1.634248e-13
[11] -2.842171e-14 5.684342e-14 0.000000e+00 -8.526513e-14 -5.684342e-14
[16] 2.842171e-14 1.421085e-13 -1.136868e-13 -2.842171e-14 4.263256e-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)
+ }
9 20
2 7
1 7
7 5
6 10
1 4
6 17
6 8
7 10
8 1
7 19
5 4
8 2
7 16
2 3
6 19
9 18
7 2
2 4
8 12
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] 3.097447
> Min(tmp)
[1] -3.108195
> mean(tmp)
[1] 0.005273392
> Sum(tmp)
[1] 0.5273392
> Var(tmp)
[1] 1.222895
>
> rowMeans(tmp)
[1] 0.005273392
> rowSums(tmp)
[1] 0.5273392
> rowVars(tmp)
[1] 1.222895
> rowSd(tmp)
[1] 1.105846
> rowMax(tmp)
[1] 3.097447
> rowMin(tmp)
[1] -3.108195
>
> colMeans(tmp)
[1] 0.800624327 0.199347057 -0.366654489 0.514002368 1.443577381
[6] 0.026097516 -1.188073924 0.096021397 0.841190340 -1.081098042
[11] -0.818712857 1.770623638 -0.944548269 0.651663551 0.798889411
[16] 0.392859005 -0.251430455 0.754335932 -0.567879522 0.428548037
[21] 0.376423214 -2.077547438 -0.565183567 2.894473941 -1.229648367
[26] -0.375656993 -0.506029018 -0.997513062 0.245568216 0.953320567
[31] -2.820243254 1.264426427 3.097447096 0.977193188 -0.313628947
[36] -0.510395968 0.978477451 -1.543144902 -0.346879821 -2.636848726
[41] 0.648837422 0.558720010 0.824959311 0.116489906 -0.842485413
[46] 0.088264168 -0.930470720 -1.128695750 0.501173667 0.151938325
[51] -0.745571088 1.541819288 0.810207158 1.174429950 0.263505913
[56] -0.087723527 0.431129678 0.508048192 -0.697353390 0.127690566
[61] -0.836837981 -0.398933662 -1.157800841 1.328701818 0.957556097
[66] 1.662421527 2.364626763 1.113588858 -1.471571597 1.267630438
[71] 1.260628620 0.257395511 -1.071603417 -0.007826839 -0.427717195
[76] -0.073453593 1.140826693 -1.051258694 -0.658856495 -2.087919487
[81] 0.260865345 0.351747780 -0.746381642 -0.317203794 1.374372048
[86] -3.108195251 -0.759627050 -0.071002720 0.015352118 -0.335673664
[91] 0.906237342 -0.782364976 0.689880663 0.138543976 -1.557751722
[96] -1.074040259 -0.786825952 0.544435549 0.753869972 -0.757401198
> colSums(tmp)
[1] 0.800624327 0.199347057 -0.366654489 0.514002368 1.443577381
[6] 0.026097516 -1.188073924 0.096021397 0.841190340 -1.081098042
[11] -0.818712857 1.770623638 -0.944548269 0.651663551 0.798889411
[16] 0.392859005 -0.251430455 0.754335932 -0.567879522 0.428548037
[21] 0.376423214 -2.077547438 -0.565183567 2.894473941 -1.229648367
[26] -0.375656993 -0.506029018 -0.997513062 0.245568216 0.953320567
[31] -2.820243254 1.264426427 3.097447096 0.977193188 -0.313628947
[36] -0.510395968 0.978477451 -1.543144902 -0.346879821 -2.636848726
[41] 0.648837422 0.558720010 0.824959311 0.116489906 -0.842485413
[46] 0.088264168 -0.930470720 -1.128695750 0.501173667 0.151938325
[51] -0.745571088 1.541819288 0.810207158 1.174429950 0.263505913
[56] -0.087723527 0.431129678 0.508048192 -0.697353390 0.127690566
[61] -0.836837981 -0.398933662 -1.157800841 1.328701818 0.957556097
[66] 1.662421527 2.364626763 1.113588858 -1.471571597 1.267630438
[71] 1.260628620 0.257395511 -1.071603417 -0.007826839 -0.427717195
[76] -0.073453593 1.140826693 -1.051258694 -0.658856495 -2.087919487
[81] 0.260865345 0.351747780 -0.746381642 -0.317203794 1.374372048
[86] -3.108195251 -0.759627050 -0.071002720 0.015352118 -0.335673664
[91] 0.906237342 -0.782364976 0.689880663 0.138543976 -1.557751722
[96] -1.074040259 -0.786825952 0.544435549 0.753869972 -0.757401198
> 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] 0.800624327 0.199347057 -0.366654489 0.514002368 1.443577381
[6] 0.026097516 -1.188073924 0.096021397 0.841190340 -1.081098042
[11] -0.818712857 1.770623638 -0.944548269 0.651663551 0.798889411
[16] 0.392859005 -0.251430455 0.754335932 -0.567879522 0.428548037
[21] 0.376423214 -2.077547438 -0.565183567 2.894473941 -1.229648367
[26] -0.375656993 -0.506029018 -0.997513062 0.245568216 0.953320567
[31] -2.820243254 1.264426427 3.097447096 0.977193188 -0.313628947
[36] -0.510395968 0.978477451 -1.543144902 -0.346879821 -2.636848726
[41] 0.648837422 0.558720010 0.824959311 0.116489906 -0.842485413
[46] 0.088264168 -0.930470720 -1.128695750 0.501173667 0.151938325
[51] -0.745571088 1.541819288 0.810207158 1.174429950 0.263505913
[56] -0.087723527 0.431129678 0.508048192 -0.697353390 0.127690566
[61] -0.836837981 -0.398933662 -1.157800841 1.328701818 0.957556097
[66] 1.662421527 2.364626763 1.113588858 -1.471571597 1.267630438
[71] 1.260628620 0.257395511 -1.071603417 -0.007826839 -0.427717195
[76] -0.073453593 1.140826693 -1.051258694 -0.658856495 -2.087919487
[81] 0.260865345 0.351747780 -0.746381642 -0.317203794 1.374372048
[86] -3.108195251 -0.759627050 -0.071002720 0.015352118 -0.335673664
[91] 0.906237342 -0.782364976 0.689880663 0.138543976 -1.557751722
[96] -1.074040259 -0.786825952 0.544435549 0.753869972 -0.757401198
> colMin(tmp)
[1] 0.800624327 0.199347057 -0.366654489 0.514002368 1.443577381
[6] 0.026097516 -1.188073924 0.096021397 0.841190340 -1.081098042
[11] -0.818712857 1.770623638 -0.944548269 0.651663551 0.798889411
[16] 0.392859005 -0.251430455 0.754335932 -0.567879522 0.428548037
[21] 0.376423214 -2.077547438 -0.565183567 2.894473941 -1.229648367
[26] -0.375656993 -0.506029018 -0.997513062 0.245568216 0.953320567
[31] -2.820243254 1.264426427 3.097447096 0.977193188 -0.313628947
[36] -0.510395968 0.978477451 -1.543144902 -0.346879821 -2.636848726
[41] 0.648837422 0.558720010 0.824959311 0.116489906 -0.842485413
[46] 0.088264168 -0.930470720 -1.128695750 0.501173667 0.151938325
[51] -0.745571088 1.541819288 0.810207158 1.174429950 0.263505913
[56] -0.087723527 0.431129678 0.508048192 -0.697353390 0.127690566
[61] -0.836837981 -0.398933662 -1.157800841 1.328701818 0.957556097
[66] 1.662421527 2.364626763 1.113588858 -1.471571597 1.267630438
[71] 1.260628620 0.257395511 -1.071603417 -0.007826839 -0.427717195
[76] -0.073453593 1.140826693 -1.051258694 -0.658856495 -2.087919487
[81] 0.260865345 0.351747780 -0.746381642 -0.317203794 1.374372048
[86] -3.108195251 -0.759627050 -0.071002720 0.015352118 -0.335673664
[91] 0.906237342 -0.782364976 0.689880663 0.138543976 -1.557751722
[96] -1.074040259 -0.786825952 0.544435549 0.753869972 -0.757401198
> colMedians(tmp)
[1] 0.800624327 0.199347057 -0.366654489 0.514002368 1.443577381
[6] 0.026097516 -1.188073924 0.096021397 0.841190340 -1.081098042
[11] -0.818712857 1.770623638 -0.944548269 0.651663551 0.798889411
[16] 0.392859005 -0.251430455 0.754335932 -0.567879522 0.428548037
[21] 0.376423214 -2.077547438 -0.565183567 2.894473941 -1.229648367
[26] -0.375656993 -0.506029018 -0.997513062 0.245568216 0.953320567
[31] -2.820243254 1.264426427 3.097447096 0.977193188 -0.313628947
[36] -0.510395968 0.978477451 -1.543144902 -0.346879821 -2.636848726
[41] 0.648837422 0.558720010 0.824959311 0.116489906 -0.842485413
[46] 0.088264168 -0.930470720 -1.128695750 0.501173667 0.151938325
[51] -0.745571088 1.541819288 0.810207158 1.174429950 0.263505913
[56] -0.087723527 0.431129678 0.508048192 -0.697353390 0.127690566
[61] -0.836837981 -0.398933662 -1.157800841 1.328701818 0.957556097
[66] 1.662421527 2.364626763 1.113588858 -1.471571597 1.267630438
[71] 1.260628620 0.257395511 -1.071603417 -0.007826839 -0.427717195
[76] -0.073453593 1.140826693 -1.051258694 -0.658856495 -2.087919487
[81] 0.260865345 0.351747780 -0.746381642 -0.317203794 1.374372048
[86] -3.108195251 -0.759627050 -0.071002720 0.015352118 -0.335673664
[91] 0.906237342 -0.782364976 0.689880663 0.138543976 -1.557751722
[96] -1.074040259 -0.786825952 0.544435549 0.753869972 -0.757401198
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] 0.8006243 0.1993471 -0.3666545 0.5140024 1.443577 0.02609752 -1.188074
[2,] 0.8006243 0.1993471 -0.3666545 0.5140024 1.443577 0.02609752 -1.188074
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] 0.0960214 0.8411903 -1.081098 -0.8187129 1.770624 -0.9445483 0.6516636
[2,] 0.0960214 0.8411903 -1.081098 -0.8187129 1.770624 -0.9445483 0.6516636
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] 0.7988894 0.392859 -0.2514305 0.7543359 -0.5678795 0.428548 0.3764232
[2,] 0.7988894 0.392859 -0.2514305 0.7543359 -0.5678795 0.428548 0.3764232
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] -2.077547 -0.5651836 2.894474 -1.229648 -0.375657 -0.506029 -0.9975131
[2,] -2.077547 -0.5651836 2.894474 -1.229648 -0.375657 -0.506029 -0.9975131
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] 0.2455682 0.9533206 -2.820243 1.264426 3.097447 0.9771932 -0.3136289
[2,] 0.2455682 0.9533206 -2.820243 1.264426 3.097447 0.9771932 -0.3136289
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] -0.510396 0.9784775 -1.543145 -0.3468798 -2.636849 0.6488374 0.55872
[2,] -0.510396 0.9784775 -1.543145 -0.3468798 -2.636849 0.6488374 0.55872
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] 0.8249593 0.1164899 -0.8424854 0.08826417 -0.9304707 -1.128696 0.5011737
[2,] 0.8249593 0.1164899 -0.8424854 0.08826417 -0.9304707 -1.128696 0.5011737
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] 0.1519383 -0.7455711 1.541819 0.8102072 1.17443 0.2635059 -0.08772353
[2,] 0.1519383 -0.7455711 1.541819 0.8102072 1.17443 0.2635059 -0.08772353
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] 0.4311297 0.5080482 -0.6973534 0.1276906 -0.836838 -0.3989337 -1.157801
[2,] 0.4311297 0.5080482 -0.6973534 0.1276906 -0.836838 -0.3989337 -1.157801
[,64] [,65] [,66] [,67] [,68] [,69] [,70] [,71]
[1,] 1.328702 0.9575561 1.662422 2.364627 1.113589 -1.471572 1.26763 1.260629
[2,] 1.328702 0.9575561 1.662422 2.364627 1.113589 -1.471572 1.26763 1.260629
[,72] [,73] [,74] [,75] [,76] [,77] [,78]
[1,] 0.2573955 -1.071603 -0.007826839 -0.4277172 -0.07345359 1.140827 -1.051259
[2,] 0.2573955 -1.071603 -0.007826839 -0.4277172 -0.07345359 1.140827 -1.051259
[,79] [,80] [,81] [,82] [,83] [,84] [,85]
[1,] -0.6588565 -2.087919 0.2608653 0.3517478 -0.7463816 -0.3172038 1.374372
[2,] -0.6588565 -2.087919 0.2608653 0.3517478 -0.7463816 -0.3172038 1.374372
[,86] [,87] [,88] [,89] [,90] [,91] [,92]
[1,] -3.108195 -0.7596271 -0.07100272 0.01535212 -0.3356737 0.9062373 -0.782365
[2,] -3.108195 -0.7596271 -0.07100272 0.01535212 -0.3356737 0.9062373 -0.782365
[,93] [,94] [,95] [,96] [,97] [,98] [,99]
[1,] 0.6898807 0.138544 -1.557752 -1.07404 -0.786826 0.5444355 0.75387
[2,] 0.6898807 0.138544 -1.557752 -1.07404 -0.786826 0.5444355 0.75387
[,100]
[1,] -0.7574012
[2,] -0.7574012
>
>
> Max(tmp2)
[1] 2.456242
> Min(tmp2)
[1] -2.286078
> mean(tmp2)
[1] -0.06733803
> Sum(tmp2)
[1] -6.733803
> Var(tmp2)
[1] 1.11079
>
> rowMeans(tmp2)
[1] -0.16864236 -0.13597377 -0.47319379 0.53793654 -0.29683754 1.10574016
[7] -0.21443582 0.86706431 1.17647920 1.14027430 0.59194604 -0.59609920
[13] 0.77970072 1.74692727 -0.08731454 0.02994746 0.84548434 0.66630016
[19] 0.24711973 -0.14030389 -0.08427155 -2.22082249 0.91983484 -0.35091903
[25] -0.48892449 1.16136170 0.05634332 0.07283045 0.75567288 2.26994797
[31] -1.37549408 -1.03054292 -0.02109670 1.30599100 0.38530377 -0.14630673
[37] -1.94541168 -2.28607773 2.45624234 -1.65399937 -1.52543456 -0.11581106
[43] 1.47206118 0.93117461 -2.09121878 1.90682779 0.69186966 -0.23773668
[49] 0.02182287 -0.60601267 -0.48658233 0.51295355 0.91131320 1.79662055
[55] -0.36001108 -0.68292377 0.05975700 -0.95581994 0.98976355 0.87804147
[61] 0.58384311 0.11476845 -0.63001492 -0.71731913 -0.30331818 -0.58682857
[67] -0.27840764 -0.50265534 1.35235193 1.31923272 0.16759966 -0.18503206
[73] -1.14828639 -1.37301671 -0.77952401 -1.40239765 -0.36986780 -0.28573503
[79] 0.01531665 -1.68302531 -0.52327203 -0.26731234 -1.09447538 -1.57910469
[85] 0.27623957 -0.40403191 0.88847581 -1.30733819 -1.61948982 -0.95941051
[91] 0.84946622 2.30547875 -1.22754770 -0.39284973 -1.93369491 0.57277204
[97] -0.09291649 -2.08421473 -0.51841791 0.55772219
> rowSums(tmp2)
[1] -0.16864236 -0.13597377 -0.47319379 0.53793654 -0.29683754 1.10574016
[7] -0.21443582 0.86706431 1.17647920 1.14027430 0.59194604 -0.59609920
[13] 0.77970072 1.74692727 -0.08731454 0.02994746 0.84548434 0.66630016
[19] 0.24711973 -0.14030389 -0.08427155 -2.22082249 0.91983484 -0.35091903
[25] -0.48892449 1.16136170 0.05634332 0.07283045 0.75567288 2.26994797
[31] -1.37549408 -1.03054292 -0.02109670 1.30599100 0.38530377 -0.14630673
[37] -1.94541168 -2.28607773 2.45624234 -1.65399937 -1.52543456 -0.11581106
[43] 1.47206118 0.93117461 -2.09121878 1.90682779 0.69186966 -0.23773668
[49] 0.02182287 -0.60601267 -0.48658233 0.51295355 0.91131320 1.79662055
[55] -0.36001108 -0.68292377 0.05975700 -0.95581994 0.98976355 0.87804147
[61] 0.58384311 0.11476845 -0.63001492 -0.71731913 -0.30331818 -0.58682857
[67] -0.27840764 -0.50265534 1.35235193 1.31923272 0.16759966 -0.18503206
[73] -1.14828639 -1.37301671 -0.77952401 -1.40239765 -0.36986780 -0.28573503
[79] 0.01531665 -1.68302531 -0.52327203 -0.26731234 -1.09447538 -1.57910469
[85] 0.27623957 -0.40403191 0.88847581 -1.30733819 -1.61948982 -0.95941051
[91] 0.84946622 2.30547875 -1.22754770 -0.39284973 -1.93369491 0.57277204
[97] -0.09291649 -2.08421473 -0.51841791 0.55772219
> rowVars(tmp2)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> rowSd(tmp2)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> rowMax(tmp2)
[1] -0.16864236 -0.13597377 -0.47319379 0.53793654 -0.29683754 1.10574016
[7] -0.21443582 0.86706431 1.17647920 1.14027430 0.59194604 -0.59609920
[13] 0.77970072 1.74692727 -0.08731454 0.02994746 0.84548434 0.66630016
[19] 0.24711973 -0.14030389 -0.08427155 -2.22082249 0.91983484 -0.35091903
[25] -0.48892449 1.16136170 0.05634332 0.07283045 0.75567288 2.26994797
[31] -1.37549408 -1.03054292 -0.02109670 1.30599100 0.38530377 -0.14630673
[37] -1.94541168 -2.28607773 2.45624234 -1.65399937 -1.52543456 -0.11581106
[43] 1.47206118 0.93117461 -2.09121878 1.90682779 0.69186966 -0.23773668
[49] 0.02182287 -0.60601267 -0.48658233 0.51295355 0.91131320 1.79662055
[55] -0.36001108 -0.68292377 0.05975700 -0.95581994 0.98976355 0.87804147
[61] 0.58384311 0.11476845 -0.63001492 -0.71731913 -0.30331818 -0.58682857
[67] -0.27840764 -0.50265534 1.35235193 1.31923272 0.16759966 -0.18503206
[73] -1.14828639 -1.37301671 -0.77952401 -1.40239765 -0.36986780 -0.28573503
[79] 0.01531665 -1.68302531 -0.52327203 -0.26731234 -1.09447538 -1.57910469
[85] 0.27623957 -0.40403191 0.88847581 -1.30733819 -1.61948982 -0.95941051
[91] 0.84946622 2.30547875 -1.22754770 -0.39284973 -1.93369491 0.57277204
[97] -0.09291649 -2.08421473 -0.51841791 0.55772219
> rowMin(tmp2)
[1] -0.16864236 -0.13597377 -0.47319379 0.53793654 -0.29683754 1.10574016
[7] -0.21443582 0.86706431 1.17647920 1.14027430 0.59194604 -0.59609920
[13] 0.77970072 1.74692727 -0.08731454 0.02994746 0.84548434 0.66630016
[19] 0.24711973 -0.14030389 -0.08427155 -2.22082249 0.91983484 -0.35091903
[25] -0.48892449 1.16136170 0.05634332 0.07283045 0.75567288 2.26994797
[31] -1.37549408 -1.03054292 -0.02109670 1.30599100 0.38530377 -0.14630673
[37] -1.94541168 -2.28607773 2.45624234 -1.65399937 -1.52543456 -0.11581106
[43] 1.47206118 0.93117461 -2.09121878 1.90682779 0.69186966 -0.23773668
[49] 0.02182287 -0.60601267 -0.48658233 0.51295355 0.91131320 1.79662055
[55] -0.36001108 -0.68292377 0.05975700 -0.95581994 0.98976355 0.87804147
[61] 0.58384311 0.11476845 -0.63001492 -0.71731913 -0.30331818 -0.58682857
[67] -0.27840764 -0.50265534 1.35235193 1.31923272 0.16759966 -0.18503206
[73] -1.14828639 -1.37301671 -0.77952401 -1.40239765 -0.36986780 -0.28573503
[79] 0.01531665 -1.68302531 -0.52327203 -0.26731234 -1.09447538 -1.57910469
[85] 0.27623957 -0.40403191 0.88847581 -1.30733819 -1.61948982 -0.95941051
[91] 0.84946622 2.30547875 -1.22754770 -0.39284973 -1.93369491 0.57277204
[97] -0.09291649 -2.08421473 -0.51841791 0.55772219
>
> colMeans(tmp2)
[1] -0.06733803
> colSums(tmp2)
[1] -6.733803
> colVars(tmp2)
[1] 1.11079
> colSd(tmp2)
[1] 1.05394
> colMax(tmp2)
[1] 2.456242
> colMin(tmp2)
[1] -2.286078
> colMedians(tmp2)
[1] -0.1381388
> colRanges(tmp2)
[,1]
[1,] -2.286078
[2,] 2.456242
>
> dataset1 <- matrix(dataset1,1,100)
>
> agree.checks(tmp,dataset1)
>
> dataset2 <- matrix(dataset2,100,1)
> agree.checks(tmp2,dataset2)
>
>
> tmp <- createBufferedMatrix(10,10)
>
> tmp[1:10,1:10] <- rnorm(100)
> colApply(tmp,sum)
[1] 2.33580085 0.01575845 -3.32787064 6.16147625 0.17334263 0.16763738
[7] 0.42933282 -0.21751922 0.91905300 -5.48720877
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.307528933
[2,] -0.007267567
[3,] 0.477531880
[4,] 0.624795224
[5,] 0.940380493
>
> rowApply(tmp,sum)
[1] -1.9308903 -0.1100597 -3.4496230 2.9926214 1.2526274 4.3409411
[7] -5.7815282 2.8842977 3.9036416 -2.9322252
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 8 5 4 7 7 6 9 9 7 6
[2,] 1 9 8 6 3 4 7 7 3 7
[3,] 3 8 5 10 1 2 2 1 9 5
[4,] 9 10 6 8 6 9 10 3 8 4
[5,] 2 6 10 1 9 7 4 2 5 1
[6,] 7 3 3 3 2 10 8 4 6 8
[7,] 10 4 2 4 4 1 5 6 10 10
[8,] 5 2 9 5 8 5 1 5 4 9
[9,] 6 1 7 9 10 3 6 8 2 3
[10,] 4 7 1 2 5 8 3 10 1 2
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] 1.237463004 -0.785359322 -4.527399272 -0.748287780 1.681844685
[6] 3.856238098 -3.899567447 -0.511103192 -0.858717671 1.010796390
[11] 4.750692545 -3.225038169 1.697908589 1.397702502 0.012950851
[16] -0.480139381 2.263144285 2.005529879 -0.002983299 1.069799252
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.2869452
[2,] -0.0969288
[3,] 0.5473860
[4,] 0.6219437
[5,] 1.4520073
>
> rowApply(tmp,sum)
[1] 1.920335 3.180494 -2.862049 5.153740 -1.447045
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 11 3 18 16 18
[2,] 9 4 11 10 12
[3,] 12 1 5 20 1
[4,] 1 11 12 14 11
[5,] 13 6 4 17 20
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] -0.0969288 -0.25228387 0.02741236 -1.6616730 0.3678578 1.4827818
[2,] -1.2869452 -1.04328158 -2.19070240 0.2836415 -0.6273421 0.2130382
[3,] 0.5473860 0.02955973 -0.64924444 0.0432733 -0.7293761 0.8360163
[4,] 0.6219437 0.42650814 1.97518785 0.5602287 0.7647938 0.5229862
[5,] 1.4520073 0.05413826 -3.69005264 0.0262417 1.9059112 0.8014156
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] -0.7193403 -0.8742853 -0.6856432 -1.4544940 2.5914686 -1.02042889
[2,] -1.4804928 0.2877624 -0.1703046 1.7659972 2.2484030 -0.03845080
[3,] -0.5606132 0.4036812 -0.2061203 -1.1922330 -0.1825220 -0.15117672
[4,] -0.8850223 0.4859886 0.7987333 0.9859879 0.5343668 -0.03064178
[5,] -0.2540989 -0.8142501 -0.5953828 0.9055382 -0.4410239 -1.98433997
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] -0.1697976 1.1529699 -0.4879424 -0.7996565 1.43247990 1.155844
[2,] 0.4008159 -0.7953777 0.3047320 0.7488074 1.79174742 0.918990
[3,] 0.2838724 1.5265983 0.3060762 0.1166508 -1.38371314 -0.382981
[4,] 0.5864252 -0.1146999 -0.9807057 -0.1843530 0.40811189 -1.491553
[5,] 0.5965927 -0.3717880 0.8707907 -0.3615882 0.01451821 1.805230
[,19] [,20]
[1,] 1.56142856 0.3705658
[2,] -0.09857678 1.9480328
[3,] 0.45772491 -1.9749087
[4,] -0.19420690 0.3636607
[5,] -1.72935310 0.3624486
>
>
> is.BufferedMatrix(tmp)
[1] TRUE
>
> as.BufferedMatrix(as.matrix(tmp))
BufferedMatrix object
Matrix size: 5 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.22-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-3.22-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-3.22-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-3.22-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
row1 -0.1723119 0.6293266 -0.4953154 -0.601991 -0.02435658 0.002912611
col7 col8 col9 col10 col11 col12 col13
row1 -0.9257028 -0.3557653 -0.326936 -1.158369 -0.6983445 -1.312051 -0.06238227
col14 col15 col16 col17 col18 col19 col20
row1 1.489961 0.00197082 0.9146993 -0.9474649 1.858701 -0.07810161 -0.56465
> tmp[,"col10"]
col10
row1 -1.15836871
row2 -0.67198998
row3 -0.33681322
row4 1.42858897
row5 0.06083294
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6
row1 -0.1723119 0.6293266 -0.4953154 -0.6019910 -0.02435658 0.002912611
row5 -0.6242118 -1.0077707 -0.8584974 -0.7877077 -0.97468524 1.130008466
col7 col8 col9 col10 col11 col12
row1 -0.9257028 -0.3557653 -0.326936 -1.15836871 -0.69834454 -1.3120506
row5 -0.2100456 -0.1443683 -1.013692 0.06083294 -0.05869382 0.4587981
col13 col14 col15 col16 col17 col18
row1 -0.06238227 1.4899613 0.00197082 0.9146993 -0.9474649 1.8587007
row5 2.11300119 0.7202228 -1.41692835 -0.2840526 1.3987207 -0.4081258
col19 col20
row1 -0.07810161 -0.564650
row5 -0.06701168 -0.535402
> tmp[,c("col6","col20")]
col6 col20
row1 0.002912611 -0.5646500
row2 2.269397934 -0.2930653
row3 -0.418591308 1.7945345
row4 0.472899907 0.1492582
row5 1.130008466 -0.5354020
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 0.002912611 -0.564650
row5 1.130008466 -0.535402
>
>
>
>
> 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 49.23441 49.60314 50.51943 52.00803 48.82517 104.2477 49.40871 51.23939
col9 col10 col11 col12 col13 col14 col15 col16
row1 51.47504 50.96341 48.51047 50.08239 49.50827 49.47374 48.20373 47.98681
col17 col18 col19 col20
row1 49.77638 49.45163 48.59701 104.0224
> tmp[,"col10"]
col10
row1 50.96341
row2 31.31214
row3 29.07290
row4 27.75849
row5 50.63159
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 49.23441 49.60314 50.51943 52.00803 48.82517 104.2477 49.40871 51.23939
row5 51.11992 49.73664 51.17206 51.06946 50.89722 106.2672 50.50085 50.67491
col9 col10 col11 col12 col13 col14 col15 col16
row1 51.47504 50.96341 48.51047 50.08239 49.50827 49.47374 48.20373 47.98681
row5 51.21596 50.63159 49.55911 50.05235 51.31720 50.24768 50.53925 49.67896
col17 col18 col19 col20
row1 49.77638 49.45163 48.59701 104.0224
row5 48.61910 51.75172 50.34849 104.2137
> tmp[,c("col6","col20")]
col6 col20
row1 104.24771 104.02244
row2 76.79493 74.47179
row3 73.95311 75.37328
row4 74.66281 75.82623
row5 106.26723 104.21367
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 104.2477 104.0224
row5 106.2672 104.2137
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 104.2477 104.0224
row5 106.2672 104.2137
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] 0.1432585
[2,] -1.6865586
[3,] -0.8377447
[4,] -0.1905077
[5,] 1.1231590
> tmp[,c("col17","col7")]
col17 col7
[1,] 0.6447869 -0.71905914
[2,] 1.4671807 -1.60657058
[3,] -2.0701793 0.91698734
[4,] 1.2012073 1.89615142
[5,] -2.5804030 -0.01981629
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] -0.43667290 0.3286115
[2,] 0.09843875 -1.0073044
[3,] -1.01473197 -1.9937009
[4,] -1.96870064 -0.9036546
[5,] -0.44631813 0.3552582
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] -0.4366729
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] -0.43667290
[2,] 0.09843875
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
>
>
>
> subBufferedMatrix(tmp,c("row3","row1"),)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6]
row3 -0.7754717 0.6376919 -0.06000948 1.191578 0.6977917 0.3890088
row1 0.8325818 -1.2244940 -1.86683133 -0.678210 1.8534504 0.2824936
[,7] [,8] [,9] [,10] [,11] [,12] [,13]
row3 -0.04037804 1.063129 -0.6566009 2.9041145 1.3930095 0.1003495 0.7505352
row1 -0.41541776 -1.144303 0.5927287 -0.6392264 0.3911426 1.1254935 -1.2564516
[,14] [,15] [,16] [,17] [,18] [,19]
row3 1.476234 -0.20612932 -0.5603006 0.4262150 -0.06974896 -0.005410106
row1 -0.780953 -0.01436791 -1.0060433 -0.4520832 2.95655013 0.518717452
[,20]
row3 1.9305958
row1 0.3870178
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 0.2689256 0.9986334 0.1776343 0.3067479 -2.207102 -1.169583 -1.261955
[,8] [,9] [,10]
row2 -0.7676541 -0.7154859 0.08952862
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 0.2125667 0.6030851 -0.8558774 0.01693224 -0.8154709 0.7767456 -1.249551
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 1.029337 -0.5069402 -1.891288 -1.268227 -1.125777 -0.5059531 -1.021973
[,15] [,16] [,17] [,18] [,19] [,20]
row5 1.430066 -0.5649393 0.817222 -0.4943482 1.237916 -0.9826124
>
>
> 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: 0x62bb57424760>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM160a3150afac38"
[2] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM160a314b1d954d"
[3] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM160a314e9fd728"
[4] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM160a3160b33f4b"
[5] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM160a317f659d3e"
[6] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM160a31588e7136"
[7] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM160a312459d468"
[8] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM160a316946dfe8"
[9] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM160a31734fe5ba"
[10] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM160a316a877941"
[11] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM160a3163eab4b0"
[12] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM160a313b603312"
[13] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM160a314ec47a2"
[14] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM160a315853f943"
[15] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM160a316abc0f6c"
>
>
> ### 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: 0x62bb59c78ac0>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x62bb59c78ac0>
Warning message:
In dir.create(new.directory) :
'/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x62bb59c78ac0>
> rowMedians(tmp)
[1] -0.565010093 -0.095360591 0.280173773 -0.511050151 -0.324993402
[6] -0.434997672 -0.244295093 0.089804551 0.372228777 -0.077299016
[11] -0.092825130 -0.177610529 -0.055433758 -0.485816102 0.265844101
[16] -0.197440293 -0.065269819 0.064677826 -0.357672837 -0.323908242
[21] 0.292493285 0.433043692 -0.117506238 -0.054369300 0.229108792
[26] -0.445110349 0.035771049 -0.230116321 0.190245320 0.468153006
[31] 0.226634628 -0.082187410 -0.228774361 -0.137564157 0.682501878
[36] 0.177887558 -0.348162752 -0.313502841 0.082114643 -0.122981240
[41] 0.311826887 -0.159699641 -0.030682626 -0.239252760 -0.120028532
[46] 0.392403694 -0.471440712 -0.323584465 -0.105784865 0.010127337
[51] -0.544888376 0.504162921 0.639127763 0.389872696 0.132422258
[56] 0.166432060 0.640181762 0.038138754 0.044705506 -0.036497943
[61] -0.018635566 0.122102466 -0.221431671 0.139097726 -0.095455871
[66] 0.156896802 -0.043179024 -0.433531673 0.736406445 0.158126262
[71] -0.386879452 0.218112124 0.456700575 -0.020067822 0.220713451
[76] -0.259555694 0.265772368 -0.047066126 -0.380455120 0.453481963
[81] 0.156196112 0.414538879 -0.149526408 -0.072503595 0.087362696
[86] 0.605117074 0.262009873 -0.643652704 -0.110789006 0.503573586
[91] 0.405969367 -0.127671917 0.434315847 -0.259128343 -0.642541196
[96] 0.154484651 -0.131064854 0.196759172 0.100275344 0.040767684
[101] -0.133061822 -0.063832550 0.071470508 0.666415894 0.289325149
[106] -0.367628082 0.347584743 -0.230816154 0.460497412 -0.263310837
[111] -0.166850394 -0.115393396 -0.255820969 0.228167284 0.065918437
[116] -0.391707270 -0.146840808 0.321490467 -0.447716256 0.863191916
[121] -0.446574888 0.431403073 -0.230298498 -0.221190622 -0.234179779
[126] 0.592911534 -0.350607803 0.190128001 -0.064462928 0.348502931
[131] 0.507124636 -0.144518556 0.591996228 -0.539655287 -0.046969480
[136] 0.024673509 -0.112023024 -0.389491993 0.253643441 0.134951859
[141] -0.333927018 0.612326223 -0.086268680 0.283865759 -0.202404402
[146] -0.168009117 0.176362243 -0.241923808 -0.387012568 -0.278367491
[151] 0.481635756 -0.255336111 0.228824346 -0.330405444 0.073110869
[156] -0.158156874 0.076120603 -0.522584890 0.022863762 -0.162972902
[161] -0.064229554 0.161995454 -0.223163111 -0.201987528 -0.184487641
[166] 0.271624320 0.116461893 0.226956558 -0.502342114 -0.008059214
[171] -0.071677356 -0.302362202 0.038412014 -0.613735113 -0.245726965
[176] -0.134079936 -0.331018155 -0.129325498 -0.232780024 -0.194827579
[181] -0.258949543 -0.103184814 0.362239809 -0.034915079 0.083933064
[186] -0.191341090 -0.521240423 -1.007044317 0.049487648 -0.159778278
[191] 0.268377590 -0.202671233 -0.088370660 0.555337306 -0.447359805
[196] -0.116598989 -0.314187382 0.044152019 0.284557451 -0.290716018
[201] -0.356564386 -0.429309284 -0.712745811 -0.062075293 -0.351070475
[206] -0.292421509 0.033143441 -0.577802695 -0.428725053 -0.610707000
[211] 0.411288461 -0.574672753 -0.311545867 -0.134537635 -0.017253900
[216] 0.406949828 0.090984056 -0.108399552 -0.029462473 -0.342421237
[221] -0.026524607 0.284619367 0.033389807 -0.070754124 -0.103943980
[226] 0.223303378 0.056747443 0.319667143 0.036883039 -0.310536366
>
> proc.time()
user system elapsed
1.269 0.639 1.896
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 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: 0x5969d7c11370>
> .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: 0x5969d7c11370>
> .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: 0x5969d7c11370>
> .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: 0x5969d7c11370>
> 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: 0x5969d7bf91c0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5969d7bf91c0>
> .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: 0x5969d7bf91c0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5969d7bf91c0>
> .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: 0x5969d7bf91c0>
> 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: 0x5969d7edc120>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5969d7edc120>
> .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: 0x5969d7edc120>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x5969d7edc120>
> .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: 0x5969d7edc120>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x5969d7edc120>
> .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: 0x5969d7edc120>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x5969d7edc120>
> .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: 0x5969d7edc120>
> 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: 0x5969d6c2c390>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x5969d6c2c390>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5969d6c2c390>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5969d6c2c390>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile160bd1141c6c66" "BufferedMatrixFile160bd14daff468"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile160bd1141c6c66" "BufferedMatrixFile160bd14daff468"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x5969d6b233d0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5969d6b233d0>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x5969d6b233d0>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x5969d6b233d0>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x5969d6b233d0>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x5969d6b233d0>
> .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: 0x5969d8658fa0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5969d8658fa0>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x5969d8658fa0>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x5969d8658fa0>
> 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: 0x5969d6e30ff0>
> .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: 0x5969d6e30ff0>
> rm(P)
>
> proc.time()
user system elapsed
0.258 0.037 0.285
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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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
0.253 0.044 0.286