Ben Bolstad
| Snapshot Date: 2026-03-08 13:45 -0400 (Sun, 08 Mar 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 -0400 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-03-09 11:57 -0400 (Mon, 09 Mar 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" | 4892 |
| 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 | | ||||||||
| 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: 1.74.0 |
| 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: 2026-03-08 21:41:00 -0400 (Sun, 08 Mar 2026) |
| EndedAt: 2026-03-08 21:41:23 -0400 (Sun, 08 Mar 2026) |
| EllapsedTime: 23.0 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
0.247 0.049 0.285
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] "Sun Mar 8 21:41:15 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] "Sun Mar 8 21:41:15 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: 0x5982bde27370>
>
>
>
> 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] "Sun Mar 8 21:41:15 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] "Sun Mar 8 21:41:15 2026"
>
> ColMode(tmp2)
<pointer: 0x5982bde27370>
>
>
>
> ### 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,] 99.1419978 -1.6195369 0.5564979 1.3991086
[2,] -1.4703490 -0.9800818 -0.1168463 -1.2583216
[3,] -0.4513966 2.2753695 -0.1431131 1.1959251
[4,] 0.1571574 0.8505773 0.5548437 -0.4716549
> 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,] 99.1419978 1.6195369 0.5564979 1.3991086
[2,] 1.4703490 0.9800818 0.1168463 1.2583216
[3,] 0.4513966 2.2753695 0.1431131 1.1959251
[4,] 0.1571574 0.8505773 0.5548437 0.4716549
> 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,] 9.9570075 1.2726103 0.7459878 1.1828392
[2,] 1.2125795 0.9899908 0.3418278 1.1217493
[3,] 0.6718606 1.5084328 0.3783029 1.0935836
[4,] 0.3964308 0.9222675 0.7448783 0.6867714
>
> 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,] 223.71207 39.34564 33.01638 38.22750
[2,] 38.59614 35.87999 28.53512 37.47581
[3,] 32.17000 42.35970 28.92614 37.13176
[4,] 29.12147 35.07325 33.00363 32.33937
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x5982bee239b0>
> exp(tmp5)
<pointer: 0x5982bee239b0>
> log(tmp5,2)
<pointer: 0x5982bee239b0>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 465.6274
> Min(tmp5)
[1] 53.46898
> mean(tmp5)
[1] 72.45341
> Sum(tmp5)
[1] 14490.68
> Var(tmp5)
[1] 853.3623
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 90.25260 71.29664 71.39278 71.36940 68.30191 68.39233 70.55634 71.37350
[9] 68.50693 73.09172
> rowSums(tmp5)
[1] 1805.052 1425.933 1427.856 1427.388 1366.038 1367.847 1411.127 1427.470
[9] 1370.139 1461.834
> rowVars(tmp5)
[1] 7876.54858 71.54298 115.67576 43.78984 97.95458 95.94403
[7] 62.09813 79.70675 55.13486 44.79548
> rowSd(tmp5)
[1] 88.749922 8.458308 10.755267 6.617390 9.897201 9.795102 7.880237
[8] 8.927864 7.425285 6.692942
> rowMax(tmp5)
[1] 465.62737 87.95760 92.08420 84.13704 92.05333 96.16555 87.01276
[8] 88.81407 84.15874 84.22095
> rowMin(tmp5)
[1] 58.67054 55.51870 53.98149 60.61251 53.46898 55.28311 58.91808 58.02812
[9] 55.00388 58.38211
>
> colMeans(tmp5)
[1] 109.28666 74.80980 69.30876 71.06228 68.82720 70.54398 66.86197
[8] 70.24919 73.31246 68.46329 67.27640 73.07194 67.66898 75.23555
[15] 70.97945 76.34472 69.07489 69.06043 64.73129 72.89908
> colSums(tmp5)
[1] 1092.8666 748.0980 693.0876 710.6228 688.2720 705.4398 668.6197
[8] 702.4919 733.1246 684.6329 672.7640 730.7194 676.6898 752.3555
[15] 709.7945 763.4472 690.7489 690.6043 647.3129 728.9908
> colVars(tmp5)
[1] 15721.05215 66.71857 120.58971 66.84811 80.45878 66.85224
[7] 70.34863 43.32134 67.99185 56.20549 57.92928 104.36291
[13] 135.75781 39.48890 67.06336 123.61829 85.47446 36.19837
[19] 42.02490 37.00825
> colSd(tmp5)
[1] 125.383620 8.168143 10.981335 8.176069 8.969882 8.176322
[7] 8.387409 6.581895 8.245717 7.497032 7.611129 10.215817
[13] 11.651516 6.284020 8.189222 11.118376 9.245240 6.016508
[19] 6.482662 6.083440
> colMax(tmp5)
[1] 465.62737 88.16616 96.16555 79.56553 80.74117 83.02216 87.00778
[8] 79.45047 92.08420 78.70416 76.15428 88.81407 92.05333 83.18100
[15] 84.22095 90.53765 80.73065 75.54734 76.82315 82.98368
> colMin(tmp5)
[1] 60.61251 61.68638 56.49565 55.19556 55.00388 58.67054 58.38211 58.85681
[9] 65.08744 58.02812 53.46898 60.68531 55.60742 61.34465 60.44617 55.28311
[17] 53.98149 59.27540 55.51870 64.02142
>
>
> ### 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] 90.25260 71.29664 71.39278 NA 68.30191 68.39233 70.55634 71.37350
[9] 68.50693 73.09172
> rowSums(tmp5)
[1] 1805.052 1425.933 1427.856 NA 1366.038 1367.847 1411.127 1427.470
[9] 1370.139 1461.834
> rowVars(tmp5)
[1] 7876.54858 71.54298 115.67576 45.25902 97.95458 95.94403
[7] 62.09813 79.70675 55.13486 44.79548
> rowSd(tmp5)
[1] 88.749922 8.458308 10.755267 6.727483 9.897201 9.795102 7.880237
[8] 8.927864 7.425285 6.692942
> rowMax(tmp5)
[1] 465.62737 87.95760 92.08420 NA 92.05333 96.16555 87.01276
[8] 88.81407 84.15874 84.22095
> rowMin(tmp5)
[1] 58.67054 55.51870 53.98149 NA 53.46898 55.28311 58.91808 58.02812
[9] 55.00388 58.38211
>
> colMeans(tmp5)
[1] 109.28666 74.80980 69.30876 NA 68.82720 70.54398 66.86197
[8] 70.24919 73.31246 68.46329 67.27640 73.07194 67.66898 75.23555
[15] 70.97945 76.34472 69.07489 69.06043 64.73129 72.89908
> colSums(tmp5)
[1] 1092.8666 748.0980 693.0876 NA 688.2720 705.4398 668.6197
[8] 702.4919 733.1246 684.6329 672.7640 730.7194 676.6898 752.3555
[15] 709.7945 763.4472 690.7489 690.6043 647.3129 728.9908
> colVars(tmp5)
[1] 15721.05215 66.71857 120.58971 NA 80.45878 66.85224
[7] 70.34863 43.32134 67.99185 56.20549 57.92928 104.36291
[13] 135.75781 39.48890 67.06336 123.61829 85.47446 36.19837
[19] 42.02490 37.00825
> colSd(tmp5)
[1] 125.383620 8.168143 10.981335 NA 8.969882 8.176322
[7] 8.387409 6.581895 8.245717 7.497032 7.611129 10.215817
[13] 11.651516 6.284020 8.189222 11.118376 9.245240 6.016508
[19] 6.482662 6.083440
> colMax(tmp5)
[1] 465.62737 88.16616 96.16555 NA 80.74117 83.02216 87.00778
[8] 79.45047 92.08420 78.70416 76.15428 88.81407 92.05333 83.18100
[15] 84.22095 90.53765 80.73065 75.54734 76.82315 82.98368
> colMin(tmp5)
[1] 60.61251 61.68638 56.49565 NA 55.00388 58.67054 58.38211 58.85681
[9] 65.08744 58.02812 53.46898 60.68531 55.60742 61.34465 60.44617 55.28311
[17] 53.98149 59.27540 55.51870 64.02142
>
> Max(tmp5,na.rm=TRUE)
[1] 465.6274
> Min(tmp5,na.rm=TRUE)
[1] 53.46898
> mean(tmp5,na.rm=TRUE)
[1] 72.47926
> Sum(tmp5,na.rm=TRUE)
[1] 14423.37
> Var(tmp5,na.rm=TRUE)
[1] 857.538
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 90.25260 71.29664 71.39278 71.58304 68.30191 68.39233 70.55634 71.37350
[9] 68.50693 73.09172
> rowSums(tmp5,na.rm=TRUE)
[1] 1805.052 1425.933 1427.856 1360.078 1366.038 1367.847 1411.127 1427.470
[9] 1370.139 1461.834
> rowVars(tmp5,na.rm=TRUE)
[1] 7876.54858 71.54298 115.67576 45.25902 97.95458 95.94403
[7] 62.09813 79.70675 55.13486 44.79548
> rowSd(tmp5,na.rm=TRUE)
[1] 88.749922 8.458308 10.755267 6.727483 9.897201 9.795102 7.880237
[8] 8.927864 7.425285 6.692942
> rowMax(tmp5,na.rm=TRUE)
[1] 465.62737 87.95760 92.08420 84.13704 92.05333 96.16555 87.01276
[8] 88.81407 84.15874 84.22095
> rowMin(tmp5,na.rm=TRUE)
[1] 58.67054 55.51870 53.98149 60.61251 53.46898 55.28311 58.91808 58.02812
[9] 55.00388 58.38211
>
> colMeans(tmp5,na.rm=TRUE)
[1] 109.28666 74.80980 69.30876 71.47918 68.82720 70.54398 66.86197
[8] 70.24919 73.31246 68.46329 67.27640 73.07194 67.66898 75.23555
[15] 70.97945 76.34472 69.07489 69.06043 64.73129 72.89908
> colSums(tmp5,na.rm=TRUE)
[1] 1092.8666 748.0980 693.0876 643.3126 688.2720 705.4398 668.6197
[8] 702.4919 733.1246 684.6329 672.7640 730.7194 676.6898 752.3555
[15] 709.7945 763.4472 690.7489 690.6043 647.3129 728.9908
> colVars(tmp5,na.rm=TRUE)
[1] 15721.05215 66.71857 120.58971 73.24878 80.45878 66.85224
[7] 70.34863 43.32134 67.99185 56.20549 57.92928 104.36291
[13] 135.75781 39.48890 67.06336 123.61829 85.47446 36.19837
[19] 42.02490 37.00825
> colSd(tmp5,na.rm=TRUE)
[1] 125.383620 8.168143 10.981335 8.558550 8.969882 8.176322
[7] 8.387409 6.581895 8.245717 7.497032 7.611129 10.215817
[13] 11.651516 6.284020 8.189222 11.118376 9.245240 6.016508
[19] 6.482662 6.083440
> colMax(tmp5,na.rm=TRUE)
[1] 465.62737 88.16616 96.16555 79.56553 80.74117 83.02216 87.00778
[8] 79.45047 92.08420 78.70416 76.15428 88.81407 92.05333 83.18100
[15] 84.22095 90.53765 80.73065 75.54734 76.82315 82.98368
> colMin(tmp5,na.rm=TRUE)
[1] 60.61251 61.68638 56.49565 55.19556 55.00388 58.67054 58.38211 58.85681
[9] 65.08744 58.02812 53.46898 60.68531 55.60742 61.34465 60.44617 55.28311
[17] 53.98149 59.27540 55.51870 64.02142
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 90.25260 71.29664 71.39278 NaN 68.30191 68.39233 70.55634 71.37350
[9] 68.50693 73.09172
> rowSums(tmp5,na.rm=TRUE)
[1] 1805.052 1425.933 1427.856 0.000 1366.038 1367.847 1411.127 1427.470
[9] 1370.139 1461.834
> rowVars(tmp5,na.rm=TRUE)
[1] 7876.54858 71.54298 115.67576 NA 97.95458 95.94403
[7] 62.09813 79.70675 55.13486 44.79548
> rowSd(tmp5,na.rm=TRUE)
[1] 88.749922 8.458308 10.755267 NA 9.897201 9.795102 7.880237
[8] 8.927864 7.425285 6.692942
> rowMax(tmp5,na.rm=TRUE)
[1] 465.62737 87.95760 92.08420 NA 92.05333 96.16555 87.01276
[8] 88.81407 84.15874 84.22095
> rowMin(tmp5,na.rm=TRUE)
[1] 58.67054 55.51870 53.98149 NA 53.46898 55.28311 58.91808 58.02812
[9] 55.00388 58.38211
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 114.69490 75.01085 69.37721 NaN 67.61765 71.23426 66.61654
[8] 70.54253 73.49126 68.27122 66.37071 74.02945 67.77534 74.74194
[15] 69.51749 75.92341 69.08784 68.41090 65.01654 72.26801
> colSums(tmp5,na.rm=TRUE)
[1] 1032.2541 675.0977 624.3949 0.0000 608.5589 641.1083 599.5488
[8] 634.8828 661.4214 614.4410 597.3364 666.2650 609.9781 672.6775
[15] 625.6574 683.3107 621.7905 615.6981 585.1489 650.4121
> colVars(tmp5,na.rm=TRUE)
[1] 17357.13197 74.60366 135.61072 NA 74.05731 69.84833
[7] 78.46457 47.76845 76.13115 62.81617 55.94227 107.09411
[13] 152.60027 41.68401 51.40153 137.07369 96.15688 35.97691
[19] 46.36261 37.15400
> colSd(tmp5,na.rm=TRUE)
[1] 131.746469 8.637341 11.645201 NA 8.605655 8.357531
[7] 8.858023 6.911472 8.725317 7.925665 7.479457 10.348629
[13] 12.353148 6.456316 7.169486 11.707847 9.805961 5.998075
[19] 6.809009 6.095408
> colMax(tmp5,na.rm=TRUE)
[1] 465.62737 88.16616 96.16555 -Inf 80.74117 83.02216 87.00778
[8] 79.45047 92.08420 78.70416 76.15428 88.81407 92.05333 83.18100
[15] 84.22095 90.53765 80.73065 75.54734 76.82315 82.98368
> colMin(tmp5,na.rm=TRUE)
[1] 63.28194 61.68638 56.49565 Inf 55.00388 58.67054 58.38211 58.85681
[9] 65.08744 58.02812 53.46898 60.68531 55.60742 61.34465 60.44617 55.28311
[17] 53.98149 59.27540 55.51870 64.02142
>
>
>
>
> 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] 264.9861 385.5576 166.9294 296.0265 300.6768 353.9893 130.0158 105.1843
[9] 190.1504 131.6403
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 264.9861 385.5576 166.9294 296.0265 300.6768 353.9893 130.0158 105.1843
[9] 190.1504 131.6403
>
>
>
> 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 5.684342e-14 -5.684342e-14 1.989520e-13
[6] -2.842171e-13 0.000000e+00 0.000000e+00 -1.421085e-13 1.136868e-13
[11] -5.684342e-14 -5.684342e-14 -1.136868e-13 1.421085e-14 -2.842171e-13
[16] 3.979039e-13 -2.273737e-13 5.684342e-14 -2.842171e-14 -2.557954e-13
>
>
>
>
>
>
>
>
>
>
> ## 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)
+ }
10 8
1 15
1 13
4 3
6 6
7 2
6 20
8 4
10 5
6 12
1 12
9 8
2 16
5 18
3 3
5 3
9 14
2 15
4 18
3 9
There were 50 or more warnings (use warnings() to see the first 50)
>
>
> ### now test 1 by n and n by 1 matrix
>
>
> err.tol <- 1e-12
>
> rm(tmp5)
>
> dataset1 <- rnorm(100)
> dataset2 <- rnorm(100)
>
> tmp <- createBufferedMatrix(1,100)
> tmp[1,] <- dataset1
>
> tmp2 <- createBufferedMatrix(100,1)
> tmp2[,1] <- dataset2
>
>
>
>
>
> Max(tmp)
[1] 2.163112
> Min(tmp)
[1] -2.018632
> mean(tmp)
[1] 0.04138925
> Sum(tmp)
[1] 4.138925
> Var(tmp)
[1] 0.9099395
>
> rowMeans(tmp)
[1] 0.04138925
> rowSums(tmp)
[1] 4.138925
> rowVars(tmp)
[1] 0.9099395
> rowSd(tmp)
[1] 0.9539075
> rowMax(tmp)
[1] 2.163112
> rowMin(tmp)
[1] -2.018632
>
> colMeans(tmp)
[1] 1.80138775 -1.06942766 1.75308399 0.66956459 -1.03619653 -0.17581495
[7] -2.01863220 -1.15723087 -1.28234341 0.66383447 1.11807221 1.45691847
[13] 0.08522978 -0.52704447 -0.44675719 -0.59288124 -0.65657534 0.73197872
[19] -1.06135818 -0.33788146 0.64598448 1.14649886 0.74867244 1.58072504
[25] -1.12497130 1.01768197 1.19053672 1.76415724 -1.00157388 0.96038831
[31] -0.09387238 1.91191691 -0.90469601 -0.63320001 0.79726762 0.17921436
[37] -1.29607580 -0.19492340 -0.47380742 0.69048883 -0.89368740 0.66214712
[43] 1.91082318 0.45802207 0.46075605 -0.04332248 -1.03744736 0.24474645
[49] 0.62470706 0.27879836 -0.89710098 0.27734618 -0.30666316 -0.35199777
[55] -0.05402520 -1.10232974 -0.73709849 -1.20618424 0.12448219 -0.85829886
[61] -0.45877751 0.36703388 0.08325627 0.17081780 -0.38110554 0.60137828
[67] 0.32908468 0.87631571 -0.54737953 0.43634580 -0.70047946 0.24892185
[73] 1.13942016 1.36426794 -1.62992205 0.34628227 -1.88099874 0.53824358
[79] 0.95598256 -1.19118741 -0.21032756 0.56321198 1.32670241 0.59290934
[85] -1.33359091 -0.41481183 1.20019987 2.16311229 0.90208316 0.51172951
[91] 0.38993905 -0.42950918 -1.11527435 -1.10603519 -0.22265455 -0.22168980
[97] 1.10151666 -0.68770419 -0.30169989 -1.61869470
> colSums(tmp)
[1] 1.80138775 -1.06942766 1.75308399 0.66956459 -1.03619653 -0.17581495
[7] -2.01863220 -1.15723087 -1.28234341 0.66383447 1.11807221 1.45691847
[13] 0.08522978 -0.52704447 -0.44675719 -0.59288124 -0.65657534 0.73197872
[19] -1.06135818 -0.33788146 0.64598448 1.14649886 0.74867244 1.58072504
[25] -1.12497130 1.01768197 1.19053672 1.76415724 -1.00157388 0.96038831
[31] -0.09387238 1.91191691 -0.90469601 -0.63320001 0.79726762 0.17921436
[37] -1.29607580 -0.19492340 -0.47380742 0.69048883 -0.89368740 0.66214712
[43] 1.91082318 0.45802207 0.46075605 -0.04332248 -1.03744736 0.24474645
[49] 0.62470706 0.27879836 -0.89710098 0.27734618 -0.30666316 -0.35199777
[55] -0.05402520 -1.10232974 -0.73709849 -1.20618424 0.12448219 -0.85829886
[61] -0.45877751 0.36703388 0.08325627 0.17081780 -0.38110554 0.60137828
[67] 0.32908468 0.87631571 -0.54737953 0.43634580 -0.70047946 0.24892185
[73] 1.13942016 1.36426794 -1.62992205 0.34628227 -1.88099874 0.53824358
[79] 0.95598256 -1.19118741 -0.21032756 0.56321198 1.32670241 0.59290934
[85] -1.33359091 -0.41481183 1.20019987 2.16311229 0.90208316 0.51172951
[91] 0.38993905 -0.42950918 -1.11527435 -1.10603519 -0.22265455 -0.22168980
[97] 1.10151666 -0.68770419 -0.30169989 -1.61869470
> colVars(tmp)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> colSd(tmp)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> colMax(tmp)
[1] 1.80138775 -1.06942766 1.75308399 0.66956459 -1.03619653 -0.17581495
[7] -2.01863220 -1.15723087 -1.28234341 0.66383447 1.11807221 1.45691847
[13] 0.08522978 -0.52704447 -0.44675719 -0.59288124 -0.65657534 0.73197872
[19] -1.06135818 -0.33788146 0.64598448 1.14649886 0.74867244 1.58072504
[25] -1.12497130 1.01768197 1.19053672 1.76415724 -1.00157388 0.96038831
[31] -0.09387238 1.91191691 -0.90469601 -0.63320001 0.79726762 0.17921436
[37] -1.29607580 -0.19492340 -0.47380742 0.69048883 -0.89368740 0.66214712
[43] 1.91082318 0.45802207 0.46075605 -0.04332248 -1.03744736 0.24474645
[49] 0.62470706 0.27879836 -0.89710098 0.27734618 -0.30666316 -0.35199777
[55] -0.05402520 -1.10232974 -0.73709849 -1.20618424 0.12448219 -0.85829886
[61] -0.45877751 0.36703388 0.08325627 0.17081780 -0.38110554 0.60137828
[67] 0.32908468 0.87631571 -0.54737953 0.43634580 -0.70047946 0.24892185
[73] 1.13942016 1.36426794 -1.62992205 0.34628227 -1.88099874 0.53824358
[79] 0.95598256 -1.19118741 -0.21032756 0.56321198 1.32670241 0.59290934
[85] -1.33359091 -0.41481183 1.20019987 2.16311229 0.90208316 0.51172951
[91] 0.38993905 -0.42950918 -1.11527435 -1.10603519 -0.22265455 -0.22168980
[97] 1.10151666 -0.68770419 -0.30169989 -1.61869470
> colMin(tmp)
[1] 1.80138775 -1.06942766 1.75308399 0.66956459 -1.03619653 -0.17581495
[7] -2.01863220 -1.15723087 -1.28234341 0.66383447 1.11807221 1.45691847
[13] 0.08522978 -0.52704447 -0.44675719 -0.59288124 -0.65657534 0.73197872
[19] -1.06135818 -0.33788146 0.64598448 1.14649886 0.74867244 1.58072504
[25] -1.12497130 1.01768197 1.19053672 1.76415724 -1.00157388 0.96038831
[31] -0.09387238 1.91191691 -0.90469601 -0.63320001 0.79726762 0.17921436
[37] -1.29607580 -0.19492340 -0.47380742 0.69048883 -0.89368740 0.66214712
[43] 1.91082318 0.45802207 0.46075605 -0.04332248 -1.03744736 0.24474645
[49] 0.62470706 0.27879836 -0.89710098 0.27734618 -0.30666316 -0.35199777
[55] -0.05402520 -1.10232974 -0.73709849 -1.20618424 0.12448219 -0.85829886
[61] -0.45877751 0.36703388 0.08325627 0.17081780 -0.38110554 0.60137828
[67] 0.32908468 0.87631571 -0.54737953 0.43634580 -0.70047946 0.24892185
[73] 1.13942016 1.36426794 -1.62992205 0.34628227 -1.88099874 0.53824358
[79] 0.95598256 -1.19118741 -0.21032756 0.56321198 1.32670241 0.59290934
[85] -1.33359091 -0.41481183 1.20019987 2.16311229 0.90208316 0.51172951
[91] 0.38993905 -0.42950918 -1.11527435 -1.10603519 -0.22265455 -0.22168980
[97] 1.10151666 -0.68770419 -0.30169989 -1.61869470
> colMedians(tmp)
[1] 1.80138775 -1.06942766 1.75308399 0.66956459 -1.03619653 -0.17581495
[7] -2.01863220 -1.15723087 -1.28234341 0.66383447 1.11807221 1.45691847
[13] 0.08522978 -0.52704447 -0.44675719 -0.59288124 -0.65657534 0.73197872
[19] -1.06135818 -0.33788146 0.64598448 1.14649886 0.74867244 1.58072504
[25] -1.12497130 1.01768197 1.19053672 1.76415724 -1.00157388 0.96038831
[31] -0.09387238 1.91191691 -0.90469601 -0.63320001 0.79726762 0.17921436
[37] -1.29607580 -0.19492340 -0.47380742 0.69048883 -0.89368740 0.66214712
[43] 1.91082318 0.45802207 0.46075605 -0.04332248 -1.03744736 0.24474645
[49] 0.62470706 0.27879836 -0.89710098 0.27734618 -0.30666316 -0.35199777
[55] -0.05402520 -1.10232974 -0.73709849 -1.20618424 0.12448219 -0.85829886
[61] -0.45877751 0.36703388 0.08325627 0.17081780 -0.38110554 0.60137828
[67] 0.32908468 0.87631571 -0.54737953 0.43634580 -0.70047946 0.24892185
[73] 1.13942016 1.36426794 -1.62992205 0.34628227 -1.88099874 0.53824358
[79] 0.95598256 -1.19118741 -0.21032756 0.56321198 1.32670241 0.59290934
[85] -1.33359091 -0.41481183 1.20019987 2.16311229 0.90208316 0.51172951
[91] 0.38993905 -0.42950918 -1.11527435 -1.10603519 -0.22265455 -0.22168980
[97] 1.10151666 -0.68770419 -0.30169989 -1.61869470
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] 1.801388 -1.069428 1.753084 0.6695646 -1.036197 -0.175815 -2.018632
[2,] 1.801388 -1.069428 1.753084 0.6695646 -1.036197 -0.175815 -2.018632
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] -1.157231 -1.282343 0.6638345 1.118072 1.456918 0.08522978 -0.5270445
[2,] -1.157231 -1.282343 0.6638345 1.118072 1.456918 0.08522978 -0.5270445
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] -0.4467572 -0.5928812 -0.6565753 0.7319787 -1.061358 -0.3378815 0.6459845
[2,] -0.4467572 -0.5928812 -0.6565753 0.7319787 -1.061358 -0.3378815 0.6459845
[,22] [,23] [,24] [,25] [,26] [,27] [,28] [,29]
[1,] 1.146499 0.7486724 1.580725 -1.124971 1.017682 1.190537 1.764157 -1.001574
[2,] 1.146499 0.7486724 1.580725 -1.124971 1.017682 1.190537 1.764157 -1.001574
[,30] [,31] [,32] [,33] [,34] [,35] [,36]
[1,] 0.9603883 -0.09387238 1.911917 -0.904696 -0.6332 0.7972676 0.1792144
[2,] 0.9603883 -0.09387238 1.911917 -0.904696 -0.6332 0.7972676 0.1792144
[,37] [,38] [,39] [,40] [,41] [,42] [,43]
[1,] -1.296076 -0.1949234 -0.4738074 0.6904888 -0.8936874 0.6621471 1.910823
[2,] -1.296076 -0.1949234 -0.4738074 0.6904888 -0.8936874 0.6621471 1.910823
[,44] [,45] [,46] [,47] [,48] [,49] [,50]
[1,] 0.4580221 0.460756 -0.04332248 -1.037447 0.2447465 0.6247071 0.2787984
[2,] 0.4580221 0.460756 -0.04332248 -1.037447 0.2447465 0.6247071 0.2787984
[,51] [,52] [,53] [,54] [,55] [,56] [,57]
[1,] -0.897101 0.2773462 -0.3066632 -0.3519978 -0.0540252 -1.10233 -0.7370985
[2,] -0.897101 0.2773462 -0.3066632 -0.3519978 -0.0540252 -1.10233 -0.7370985
[,58] [,59] [,60] [,61] [,62] [,63] [,64]
[1,] -1.206184 0.1244822 -0.8582989 -0.4587775 0.3670339 0.08325627 0.1708178
[2,] -1.206184 0.1244822 -0.8582989 -0.4587775 0.3670339 0.08325627 0.1708178
[,65] [,66] [,67] [,68] [,69] [,70] [,71]
[1,] -0.3811055 0.6013783 0.3290847 0.8763157 -0.5473795 0.4363458 -0.7004795
[2,] -0.3811055 0.6013783 0.3290847 0.8763157 -0.5473795 0.4363458 -0.7004795
[,72] [,73] [,74] [,75] [,76] [,77] [,78]
[1,] 0.2489219 1.13942 1.364268 -1.629922 0.3462823 -1.880999 0.5382436
[2,] 0.2489219 1.13942 1.364268 -1.629922 0.3462823 -1.880999 0.5382436
[,79] [,80] [,81] [,82] [,83] [,84] [,85]
[1,] 0.9559826 -1.191187 -0.2103276 0.563212 1.326702 0.5929093 -1.333591
[2,] 0.9559826 -1.191187 -0.2103276 0.563212 1.326702 0.5929093 -1.333591
[,86] [,87] [,88] [,89] [,90] [,91] [,92]
[1,] -0.4148118 1.2002 2.163112 0.9020832 0.5117295 0.389939 -0.4295092
[2,] -0.4148118 1.2002 2.163112 0.9020832 0.5117295 0.389939 -0.4295092
[,93] [,94] [,95] [,96] [,97] [,98] [,99]
[1,] -1.115274 -1.106035 -0.2226545 -0.2216898 1.101517 -0.6877042 -0.3016999
[2,] -1.115274 -1.106035 -0.2226545 -0.2216898 1.101517 -0.6877042 -0.3016999
[,100]
[1,] -1.618695
[2,] -1.618695
>
>
> Max(tmp2)
[1] 1.959548
> Min(tmp2)
[1] -3.399929
> mean(tmp2)
[1] -0.1218033
> Sum(tmp2)
[1] -12.18033
> Var(tmp2)
[1] 0.8037628
>
> rowMeans(tmp2)
[1] 1.316016416 1.338948835 -0.789518007 -0.418161627 -0.029045330
[6] -0.389379556 -0.382320945 -0.947345554 0.895885386 -1.967697238
[11] 0.197561941 -0.629535663 0.293800419 -0.971255629 -0.729850655
[16] 0.012597757 1.173595640 0.588709355 0.310246534 0.359102641
[21] -0.230295234 1.759590148 -0.106063100 0.095582053 1.372068152
[26] -1.893568676 0.361663646 -0.513036260 0.194412439 0.367010792
[31] -0.907011625 0.310272496 1.438889973 0.667573872 -0.535790743
[36] -0.086063126 -0.375296371 0.182467355 0.632450496 -0.235668960
[41] -0.768139649 -0.027495301 0.330629327 -0.217467037 -0.629970076
[46] -0.689805193 -0.432512949 -0.839674579 1.244045973 -0.885817367
[51] 0.398466361 -0.602732555 1.391471713 -1.104997020 0.659293203
[56] -0.575431884 -0.033791531 -1.534497294 -0.129945872 1.805908387
[61] 0.567282752 -0.609724702 0.730390278 -1.041796821 -0.006770743
[66] -0.895085882 1.033818897 0.547429245 -0.423796055 0.646289660
[71] -0.965046198 0.339804446 -0.881311419 -0.442193992 -0.663514595
[76] -1.414864824 -1.625821079 -1.200478347 -3.399929192 -0.062784964
[81] -1.387199944 0.497152603 1.459217432 1.959548343 -0.220827358
[86] -0.811004788 -0.168085918 -0.264478858 -0.274629042 -0.618257042
[91] -0.679233802 -0.026258414 -0.615538742 -1.252962889 0.546414478
[96] 0.434669447 0.298348744 0.555645625 -0.237534565 -0.696290932
> rowSums(tmp2)
[1] 1.316016416 1.338948835 -0.789518007 -0.418161627 -0.029045330
[6] -0.389379556 -0.382320945 -0.947345554 0.895885386 -1.967697238
[11] 0.197561941 -0.629535663 0.293800419 -0.971255629 -0.729850655
[16] 0.012597757 1.173595640 0.588709355 0.310246534 0.359102641
[21] -0.230295234 1.759590148 -0.106063100 0.095582053 1.372068152
[26] -1.893568676 0.361663646 -0.513036260 0.194412439 0.367010792
[31] -0.907011625 0.310272496 1.438889973 0.667573872 -0.535790743
[36] -0.086063126 -0.375296371 0.182467355 0.632450496 -0.235668960
[41] -0.768139649 -0.027495301 0.330629327 -0.217467037 -0.629970076
[46] -0.689805193 -0.432512949 -0.839674579 1.244045973 -0.885817367
[51] 0.398466361 -0.602732555 1.391471713 -1.104997020 0.659293203
[56] -0.575431884 -0.033791531 -1.534497294 -0.129945872 1.805908387
[61] 0.567282752 -0.609724702 0.730390278 -1.041796821 -0.006770743
[66] -0.895085882 1.033818897 0.547429245 -0.423796055 0.646289660
[71] -0.965046198 0.339804446 -0.881311419 -0.442193992 -0.663514595
[76] -1.414864824 -1.625821079 -1.200478347 -3.399929192 -0.062784964
[81] -1.387199944 0.497152603 1.459217432 1.959548343 -0.220827358
[86] -0.811004788 -0.168085918 -0.264478858 -0.274629042 -0.618257042
[91] -0.679233802 -0.026258414 -0.615538742 -1.252962889 0.546414478
[96] 0.434669447 0.298348744 0.555645625 -0.237534565 -0.696290932
> 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] 1.316016416 1.338948835 -0.789518007 -0.418161627 -0.029045330
[6] -0.389379556 -0.382320945 -0.947345554 0.895885386 -1.967697238
[11] 0.197561941 -0.629535663 0.293800419 -0.971255629 -0.729850655
[16] 0.012597757 1.173595640 0.588709355 0.310246534 0.359102641
[21] -0.230295234 1.759590148 -0.106063100 0.095582053 1.372068152
[26] -1.893568676 0.361663646 -0.513036260 0.194412439 0.367010792
[31] -0.907011625 0.310272496 1.438889973 0.667573872 -0.535790743
[36] -0.086063126 -0.375296371 0.182467355 0.632450496 -0.235668960
[41] -0.768139649 -0.027495301 0.330629327 -0.217467037 -0.629970076
[46] -0.689805193 -0.432512949 -0.839674579 1.244045973 -0.885817367
[51] 0.398466361 -0.602732555 1.391471713 -1.104997020 0.659293203
[56] -0.575431884 -0.033791531 -1.534497294 -0.129945872 1.805908387
[61] 0.567282752 -0.609724702 0.730390278 -1.041796821 -0.006770743
[66] -0.895085882 1.033818897 0.547429245 -0.423796055 0.646289660
[71] -0.965046198 0.339804446 -0.881311419 -0.442193992 -0.663514595
[76] -1.414864824 -1.625821079 -1.200478347 -3.399929192 -0.062784964
[81] -1.387199944 0.497152603 1.459217432 1.959548343 -0.220827358
[86] -0.811004788 -0.168085918 -0.264478858 -0.274629042 -0.618257042
[91] -0.679233802 -0.026258414 -0.615538742 -1.252962889 0.546414478
[96] 0.434669447 0.298348744 0.555645625 -0.237534565 -0.696290932
> rowMin(tmp2)
[1] 1.316016416 1.338948835 -0.789518007 -0.418161627 -0.029045330
[6] -0.389379556 -0.382320945 -0.947345554 0.895885386 -1.967697238
[11] 0.197561941 -0.629535663 0.293800419 -0.971255629 -0.729850655
[16] 0.012597757 1.173595640 0.588709355 0.310246534 0.359102641
[21] -0.230295234 1.759590148 -0.106063100 0.095582053 1.372068152
[26] -1.893568676 0.361663646 -0.513036260 0.194412439 0.367010792
[31] -0.907011625 0.310272496 1.438889973 0.667573872 -0.535790743
[36] -0.086063126 -0.375296371 0.182467355 0.632450496 -0.235668960
[41] -0.768139649 -0.027495301 0.330629327 -0.217467037 -0.629970076
[46] -0.689805193 -0.432512949 -0.839674579 1.244045973 -0.885817367
[51] 0.398466361 -0.602732555 1.391471713 -1.104997020 0.659293203
[56] -0.575431884 -0.033791531 -1.534497294 -0.129945872 1.805908387
[61] 0.567282752 -0.609724702 0.730390278 -1.041796821 -0.006770743
[66] -0.895085882 1.033818897 0.547429245 -0.423796055 0.646289660
[71] -0.965046198 0.339804446 -0.881311419 -0.442193992 -0.663514595
[76] -1.414864824 -1.625821079 -1.200478347 -3.399929192 -0.062784964
[81] -1.387199944 0.497152603 1.459217432 1.959548343 -0.220827358
[86] -0.811004788 -0.168085918 -0.264478858 -0.274629042 -0.618257042
[91] -0.679233802 -0.026258414 -0.615538742 -1.252962889 0.546414478
[96] 0.434669447 0.298348744 0.555645625 -0.237534565 -0.696290932
>
> colMeans(tmp2)
[1] -0.1218033
> colSums(tmp2)
[1] -12.18033
> colVars(tmp2)
[1] 0.8037628
> colSd(tmp2)
[1] 0.8965282
> colMax(tmp2)
[1] 1.959548
> colMin(tmp2)
[1] -3.399929
> colMedians(tmp2)
[1] -0.1927765
> colRanges(tmp2)
[,1]
[1,] -3.399929
[2,] 1.959548
>
> 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] -4.7371581 0.5606035 -0.8073554 -0.2473219 -2.5124981 -0.5170813
[7] -0.3001659 -2.8068671 0.6746141 -0.5826182
> colApply(tmp,quantile)[,1]
[,1]
[1,] -2.3968898
[2,] -1.5980188
[3,] -0.2909721
[4,] 0.3314397
[5,] 1.8960722
>
> rowApply(tmp,sum)
[1] -1.7951453 -1.5327923 -3.3042721 -3.0333563 -3.0737168 -1.8053761
[7] -0.3861554 -0.2483923 3.7712590 0.1320992
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 3 1 1 10 2 1 8 8 6 7
[2,] 8 6 5 5 7 5 6 3 8 8
[3,] 6 8 4 2 9 9 2 1 9 9
[4,] 10 7 9 1 8 4 3 7 2 1
[5,] 1 4 7 3 3 7 7 9 5 4
[6,] 2 10 8 4 5 6 9 5 3 6
[7,] 5 3 6 7 10 8 5 2 4 2
[8,] 9 9 3 9 4 10 1 6 1 3
[9,] 7 2 2 8 1 3 10 10 7 10
[10,] 4 5 10 6 6 2 4 4 10 5
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] -0.81431529 1.91905053 -0.86798847 0.56683927 0.02584164 -1.00710082
[7] 5.36613356 -3.42653485 4.83091580 -1.41063769 1.52047625 1.40715617
[13] -2.14487772 0.86848502 0.02401770 1.37908538 -0.49822514 -0.20085538
[19] -0.25803461 -1.36569187
> colApply(tmp,quantile)[,1]
[,1]
[1,] -2.35483356
[2,] -0.05821742
[3,] 0.23285628
[4,] 0.41645154
[5,] 0.94942788
>
> rowApply(tmp,sum)
[1] -2.138772 -2.931053 1.750320 6.291093 2.942153
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 12 10 11 1 16
[2,] 11 16 8 15 13
[3,] 14 20 2 3 4
[4,] 6 15 4 14 14
[5,] 2 2 6 16 18
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 0.23285628 0.03700308 0.4530493 -0.8293536 -1.4559764 -2.52168326
[2,] -0.05821742 0.34993899 1.4920261 0.2985175 -1.5167075 1.23366628
[3,] 0.41645154 -0.22111301 -1.0578342 -0.6355389 -0.4937573 -0.95262772
[4,] -2.35483356 1.18435199 -0.5892652 1.0731244 1.4268750 0.02660481
[5,] 0.94942788 0.56886947 -1.1659645 0.6600899 2.0654079 1.20693908
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] -0.84458533 -0.02524778 0.7176200 -1.2528523 -0.9004345 -0.31543527
[2,] 0.07191868 -0.53076540 0.1451703 -0.6937699 0.5994503 -0.31703507
[3,] 0.87143390 -1.81345464 0.9950658 0.2092086 0.9853122 0.09344294
[4,] 2.12812774 -0.36423856 2.1618805 0.7708385 1.5929766 -0.21884574
[5,] 3.13923857 -0.69282848 0.8111791 -0.4440627 -0.7568284 2.16502930
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] 0.4987274 0.3438763 -0.34388229 1.5418823 0.9531222 -0.6017875
[2,] -2.5189094 0.4872170 0.23693879 -0.7687439 -0.4491715 -0.4175691
[3,] 0.8695881 0.7775109 0.58189326 0.5262038 0.7610999 0.8994485
[4,] 0.2021057 -0.2148207 -0.52140960 1.5266856 0.2158478 -0.2807659
[5,] -1.1963896 -0.5252985 0.07047754 -1.4469425 -1.9791235 0.1998186
[,19] [,20]
[1,] 1.2796034 0.89472560
[2,] -0.5528179 -0.02219018
[3,] -0.4789522 -0.58306208
[4,] -0.3403791 -1.13376765
[5,] -0.1654889 -0.52139756
>
>
> 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 : 654 bytes.
Disk usage : 200 bytes.
> subBufferedMatrix(tmp,,5:8)
BufferedMatrix object
Matrix size: 5 4
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.22-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 col7
row1 0.3898071 -0.4923903 0.2976254 0.5804758 0.3419537 0.4318185 1.641888
col8 col9 col10 col11 col12 col13 col14
row1 0.1974672 -0.3509348 0.149834 -0.7297404 0.7055282 -0.6140049 0.7548232
col15 col16 col17 col18 col19 col20
row1 -0.9542873 -1.898712 0.9905841 -1.368199 0.03755244 1.496803
> tmp[,"col10"]
col10
row1 0.1498340
row2 -0.4819209
row3 0.4889822
row4 1.4321917
row5 1.0184534
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6
row1 0.3898071 -0.4923903 0.29762543 0.5804758 0.3419537 0.4318185
row5 -0.3490380 -0.5707083 -0.05299974 -0.0518994 1.2178448 -0.4487051
col7 col8 col9 col10 col11 col12 col13
row1 1.641888 0.1974672 -0.3509348 0.149834 -0.72974040 0.7055282 -0.6140049
row5 -0.382546 0.9458736 0.3381328 1.018453 0.08517635 -0.3407413 1.9672081
col14 col15 col16 col17 col18 col19
row1 0.7548232 -0.9542873 -1.8987123 0.9905841 -1.3681986 0.03755244
row5 0.8566124 -2.2166519 0.2294728 -1.6967650 0.1545182 0.62007942
col20
row1 1.4968031
row5 -0.3824135
> tmp[,c("col6","col20")]
col6 col20
row1 0.4318185 1.4968031
row2 0.4508665 -0.3406970
row3 -0.3063594 -1.3345210
row4 1.7835044 0.2822501
row5 -0.4487051 -0.3824135
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 0.4318185 1.4968031
row5 -0.4487051 -0.3824135
>
>
>
>
> 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 49.49217 48.86397 48.8132 50.8529 48.96841 104.1485 51.31098 49.86407
col9 col10 col11 col12 col13 col14 col15 col16
row1 50.02072 49.41287 50.91863 50.4176 48.70435 50.13292 50.46801 49.85392
col17 col18 col19 col20
row1 49.2527 48.38067 51.80335 105.4501
> tmp[,"col10"]
col10
row1 49.41287
row2 29.91398
row3 29.37871
row4 28.99228
row5 48.65878
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 49.49217 48.86397 48.81320 50.85290 48.96841 104.1485 51.31098 49.86407
row5 50.58422 50.04104 50.40081 48.81693 49.04112 105.7547 49.65236 50.02727
col9 col10 col11 col12 col13 col14 col15 col16
row1 50.02072 49.41287 50.91863 50.41760 48.70435 50.13292 50.46801 49.85392
row5 49.05711 48.65878 49.51156 49.05868 50.15005 50.32191 49.50625 49.29806
col17 col18 col19 col20
row1 49.25270 48.38067 51.80335 105.4501
row5 51.80399 48.78340 51.63143 106.1678
> tmp[,c("col6","col20")]
col6 col20
row1 104.14847 105.45008
row2 75.97192 73.69479
row3 73.92393 73.44810
row4 74.43198 75.35591
row5 105.75470 106.16777
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 104.1485 105.4501
row5 105.7547 106.1678
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 104.1485 105.4501
row5 105.7547 106.1678
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] -0.7167915
[2,] -0.9175373
[3,] 0.1515561
[4,] -0.3241560
[5,] -1.1207396
> tmp[,c("col17","col7")]
col17 col7
[1,] 0.4145229 -0.6861469
[2,] 1.0926116 0.6333241
[3,] 0.8599172 -0.7439911
[4,] -0.2470070 1.6974346
[5,] -0.7125204 1.3133651
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] -0.2991593 0.9396108
[2,] 0.6298317 -0.1497850
[3,] 0.5958273 0.2267793
[4,] -0.3413718 -0.3048650
[5,] 0.3569059 -0.5720358
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] -0.2991593
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] -0.2991593
[2,] 0.6298317
>
>
>
> 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 -1.535127 -0.80928753 0.5071230 0.2182529 1.23317617 0.1785814
row1 -0.442251 0.09692426 -0.4073697 -1.0280672 -0.03800219 -0.3422375
[,7] [,8] [,9] [,10] [,11] [,12]
row3 -0.09915518 0.6801458 0.1928565 -1.727412 1.1248235 -0.2324901
row1 0.19021883 -1.1033526 -0.9285662 -1.097524 0.3369994 -2.4322215
[,13] [,14] [,15] [,16] [,17] [,18]
row3 -2.3480254 -1.1910376 0.1837135 -0.02517115 -0.1402788 -1.2826151
row1 0.4120368 -0.1714478 0.9458616 -0.24702001 -0.3392852 0.6765018
[,19] [,20]
row3 -1.9017314 0.5147448
row1 0.1551852 -0.7341476
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 -0.4530298 -0.004054083 -0.8656239 -0.7078592 1.269353 0.2924577 0.4029767
[,8] [,9] [,10]
row2 -0.7221859 0.1536933 0.6127935
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 0.4288769 -2.613915 -0.1927355 -0.9104414 -0.8978013 -0.378424 -0.4039386
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 -0.2151574 -1.915986 0.227061 1.115466 -0.2637249 0.1498198 1.051753
[,15] [,16] [,17] [,18] [,19] [,20]
row5 -0.5091137 -2.168551 1.41557 0.09996851 0.7033041 -1.405428
>
>
> 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: 0x5982beaccca0>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1f89932ab5a1ee"
[2] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1f89934fefe89d"
[3] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1f89934155b3e9"
[4] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1f8993739fe106"
[5] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1f899344d4c753"
[6] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1f899321fe7433"
[7] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1f899327f0d89d"
[8] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1f89931e35f4f8"
[9] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1f899374fc412c"
[10] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1f8993527f54bc"
[11] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1f8993781c3148"
[12] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1f89936d0beab1"
[13] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1f899348caef56"
[14] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1f899361e67a1e"
[15] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM1f8993b074d67"
>
>
> ### 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: 0x5982bf376220>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x5982bf376220>
Warning message:
In dir.create(new.directory) :
'/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x5982bf376220>
> rowMedians(tmp)
[1] -0.0861116975 -0.4141867257 0.0751336488 0.3354978352 0.1134560033
[6] -0.3032579693 0.0752514469 -0.3521578263 0.3728157441 0.2388341920
[11] 0.0833480567 0.1471051920 -0.2916464724 0.1634694192 0.2842306815
[16] 0.4107030750 0.0386872070 -0.0539747828 0.0642098230 -0.2473153751
[21] 0.1153832950 -0.2045306531 0.2521648511 0.2707757472 -0.2600145069
[26] -0.4136320819 0.1797203807 -0.0909801429 0.1336545667 -0.0339533013
[31] 0.0421577453 0.5416831939 -0.1632328863 0.0925906389 -0.1560543484
[36] 0.1671857844 0.0067285957 0.0783975799 0.3082238685 0.3489847674
[41] 0.0006320546 0.3584994748 0.0913377068 0.7037969282 -0.1185518230
[46] 0.1416632139 -0.1790154580 0.1281541486 0.0972129546 -0.6474329346
[51] -0.4915688698 0.4201389728 -0.1101238643 -0.3484040833 -0.3039494336
[56] 0.1989466473 0.3134139311 0.1968304527 -0.4891054005 -0.3365640026
[61] 0.0305656438 -0.3338746390 -0.2358547244 0.3137403393 -0.0160159906
[66] 0.5065136345 -0.0187523782 -0.6332345011 0.5339000981 0.4632967466
[71] 0.0112892205 -0.2534212903 -0.5017210068 -0.1510006622 0.2382191895
[76] -0.1943140453 0.4114585319 0.2603172889 0.3427418112 0.0911322141
[81] 0.3648511435 0.2980544601 0.0172794502 0.0911896680 0.2132608510
[86] -0.0013684163 -0.1061303953 -0.0835177733 0.3844947029 0.1143568793
[91] -0.1419709670 0.0458476594 -0.4670169279 0.1309023100 -0.1473392872
[96] -0.2547026244 0.0148095107 0.6606662529 0.0480680424 0.1431435014
[101] -0.6329447746 -0.1052350024 -0.2343397679 0.1289826267 0.3861968468
[106] 0.2217724039 -0.5014145045 0.1056824361 0.2091664701 0.3849287750
[111] -0.0509499481 -0.3743628120 -0.1443633500 -0.4131300651 0.3329474057
[116] -0.0947422249 0.2697783710 0.1189706149 0.0318828363 0.5545861816
[121] -0.3614707835 -0.3516894180 0.0457538275 0.0748208106 -0.2528506528
[126] -0.2909798445 -0.1740250913 0.0513638821 0.3467382052 0.2287980388
[131] -0.1942097894 0.0530466037 -0.1090993436 -0.0195981867 -0.2009660616
[136] -0.0054980935 0.3866978021 -0.0739088130 0.8172463851 -0.2319867561
[141] 0.2114630356 0.2176293093 0.3771570944 0.2717879928 -0.0362387985
[146] 0.0210628724 -0.6252145221 0.2578806491 -0.0647557377 0.4918856106
[151] -0.3846085046 0.7757176689 0.1228243907 0.0434892862 -0.3765176060
[156] 0.2242658227 0.4343953328 -0.1986745070 0.2044182884 -0.0370793927
[161] -0.3050196134 -0.3493408376 0.1300852027 -0.0557273520 -0.1374689623
[166] -0.3071917071 -0.0551386397 -0.1239186688 0.4377585911 -0.0144519417
[171] 0.8068008862 -0.8018572959 0.0632214643 -0.4118957979 -0.2701441507
[176] -0.2406967352 -0.6825596075 -0.2994225590 0.1219678480 0.2679477838
[181] -0.1505003708 0.0103308573 0.3895123749 0.4951271503 -0.3074995778
[186] -0.0238291966 0.1113822020 0.0847157156 -0.2660768117 -0.0151109591
[191] 0.0822014208 0.1308533821 0.6844735022 0.2601644173 -0.3263773514
[196] -0.1335905907 -0.0042303036 -0.6909151586 -0.4430692319 0.1544206701
[201] 0.2208246936 0.4545428233 -0.4235269004 0.4307913979 0.0417534127
[206] 0.0473867165 -0.3243013101 -0.3574641160 0.0632414214 0.5708479114
[211] 0.6421532169 0.2669870961 0.1261892739 0.3218869023 0.3182601281
[216] -0.3637954798 0.2986719871 0.2752068366 -0.1343521405 0.3674134909
[221] 0.4671335891 -0.4565549363 0.0733523487 -0.3187874901 -0.0585513211
[226] -0.4550451581 -0.5011564452 0.1893626462 -0.2636950847 0.1096048993
>
> proc.time()
user system elapsed
1.264 0.678 1.930
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: 0x5e9e85fdf370>
> .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: 0x5e9e85fdf370>
> .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: 0x5e9e85fdf370>
> .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: 0x5e9e85fdf370>
> 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: 0x5e9e85fc71c0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5e9e85fc71c0>
> .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: 0x5e9e85fc71c0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5e9e85fc71c0>
> .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: 0x5e9e85fc71c0>
> 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: 0x5e9e862aa120>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5e9e862aa120>
> .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: 0x5e9e862aa120>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x5e9e862aa120>
> .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: 0x5e9e862aa120>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x5e9e862aa120>
> .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: 0x5e9e862aa120>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x5e9e862aa120>
> .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: 0x5e9e862aa120>
> 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: 0x5e9e84ffa390>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x5e9e84ffa390>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5e9e84ffa390>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5e9e84ffa390>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile1f8b05418c91e7" "BufferedMatrixFile1f8b05545f8c81"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile1f8b05418c91e7" "BufferedMatrixFile1f8b05545f8c81"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x5e9e84ef13d0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5e9e84ef13d0>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x5e9e84ef13d0>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x5e9e84ef13d0>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x5e9e84ef13d0>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x5e9e84ef13d0>
> .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: 0x5e9e86a26fa0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5e9e86a26fa0>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x5e9e86a26fa0>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x5e9e86a26fa0>
> 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: 0x5e9e851feff0>
> .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: 0x5e9e851feff0>
> rm(P)
>
> proc.time()
user system elapsed
0.259 0.043 0.291
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
0.250 0.042 0.282