Ben Bolstad
| Snapshot Date: 2025-10-30 13:40 -0400 (Thu, 30 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/BufferedMatrix |
| git_branch: devel |
| git_last_commit: ecdbf23 |
| git_last_commit_date: 2025-10-29 09:58:55 -0400 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-10-31 08:34 -0400 (Fri, 31 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4428 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 251/2321 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BufferedMatrix 1.75.0 (landing page) Ben Bolstad
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the BufferedMatrix package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BufferedMatrix.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BufferedMatrix |
| Version: 1.75.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BufferedMatrix_1.75.0.tar.gz |
| StartedAt: 2025-10-30 20:13:16 -0400 (Thu, 30 Oct 2025) |
| EndedAt: 2025-10-30 20:13:40 -0400 (Thu, 30 Oct 2025) |
| EllapsedTime: 24.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BufferedMatrix_1.75.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 ‘1.75.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BufferedMatrix’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) BufferedMatrix-class.Rd:209: Lost braces; missing escapes or markup?
209 | $x^{power}$ elementwise of the matrix
| ^
prepare_Rd: createBufferedMatrix.Rd:26: Dropping empty section \keyword
prepare_Rd: createBufferedMatrix.Rd:17-18: Dropping empty section \details
prepare_Rd: createBufferedMatrix.Rd:15-16: Dropping empty section \value
prepare_Rd: createBufferedMatrix.Rd:19-20: Dropping empty section \references
prepare_Rd: createBufferedMatrix.Rd:21-22: Dropping empty section \seealso
prepare_Rd: createBufferedMatrix.Rd:23-24: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... INFO
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ...* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘Rcodetesting.R’
Running ‘c_code_level_tests.R’
Running ‘objectTesting.R’
Running ‘rawCalltesting.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/00check.log’
for details.
BufferedMatrix.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL BufferedMatrix
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘BufferedMatrix’ ...
** this is package ‘BufferedMatrix’ version ‘1.75.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RBufferedMatrix.c -o RBufferedMatrix.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c doubleBufferedMatrix.c -o doubleBufferedMatrix.o
doubleBufferedMatrix.c: In function ‘dbm_ReadOnlyMode’:
doubleBufferedMatrix.c:1580:7: warning: suggest parentheses around operand of ‘!’ or change ‘&’ to ‘&&’ or ‘!’ to ‘~’ [-Wparentheses]
1580 | if (!(Matrix->readonly) & setting){
| ^~~~~~~~~~~~~~~~~~~
doubleBufferedMatrix.c: At top level:
doubleBufferedMatrix.c:3327:12: warning: ‘sort_double’ defined but not used [-Wunused-function]
3327 | static int sort_double(const double *a1,const double *a2){
| ^~~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c doubleBufferedMatrix_C_tests.c -o doubleBufferedMatrix_C_tests.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c init_package.c -o init_package.o
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o BufferedMatrix.so RBufferedMatrix.o doubleBufferedMatrix.o doubleBufferedMatrix_C_tests.o init_package.o -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-BufferedMatrix/00new/BufferedMatrix/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘rowMeans’ in package ‘BufferedMatrix’
Creating a new generic function for ‘rowSums’ in package ‘BufferedMatrix’
Creating a new generic function for ‘colMeans’ in package ‘BufferedMatrix’
Creating a new generic function for ‘colSums’ in package ‘BufferedMatrix’
Creating a generic function for ‘ncol’ from package ‘base’ in package ‘BufferedMatrix’
Creating a generic function for ‘nrow’ from package ‘base’ in package ‘BufferedMatrix’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BufferedMatrix)
BufferedMatrix.Rcheck/tests/c_code_level_tests.Rout
R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
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
0.240 0.054 0.283
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
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-3.23-bioc/meat/BufferedMatrix.Rcheck/tests"
> prefix(tmp3)
[1] "BM"
>
> ## testing if we can remove these objects
> rm(tmp, tmp2, tmp3)
> gc()
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 478818 25.6 1048392 56 639317 34.2
Vcells 885623 6.8 8388608 64 2082728 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] "Thu Oct 30 20:13:31 2025"
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
> date()
[1] "Thu Oct 30 20:13:31 2025"
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,which.col] == test.matrix[which.row,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
>
>
> RowMode(tmp2)
<pointer: 0x620fcc8c35e0>
>
>
>
> 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] "Thu Oct 30 20:13:31 2025"
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[which.row,which.col] == test.matrix[which.row,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
> date()
[1] "Thu Oct 30 20:13:32 2025"
>
> ColMode(tmp2)
<pointer: 0x620fcc8c35e0>
>
>
>
> ### 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,] 99.2092306 0.3534756 0.8750370 -0.1840163
[2,] 1.1361947 -1.0253958 -0.6813963 -1.5284967
[3,] -0.4362007 -0.2011854 0.9486364 -1.2395358
[4,] 0.1248146 -0.7824675 2.4279591 -0.2714064
> ewApply(tmp5,abs)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 99.2092306 0.3534756 0.8750370 0.1840163
[2,] 1.1361947 1.0253958 0.6813963 1.5284967
[3,] 0.4362007 0.2011854 0.9486364 1.2395358
[4,] 0.1248146 0.7824675 2.4279591 0.2714064
> ewApply(tmp5,sqrt)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 9.9603831 0.5945382 0.9354341 0.4289712
[2,] 1.0659244 1.0126183 0.8254673 1.2363239
[3,] 0.6604549 0.4485370 0.9739797 1.1133444
[4,] 0.3532910 0.8845719 1.5581910 0.5209668
>
> my.function <- function(x,power){
+ (x+5)^power
+ }
>
> ewApply(tmp5,my.function,power=2)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 223.81306 31.29886 35.22938 29.47373
[2,] 36.79544 36.15158 33.93607 38.89174
[3,] 32.04075 29.68656 35.68843 37.37298
[4,] 28.65772 34.62819 43.00987 30.48107
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x620fcc44e840>
> exp(tmp5)
<pointer: 0x620fcc44e840>
> log(tmp5,2)
<pointer: 0x620fcc44e840>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 465.8376
> Min(tmp5)
[1] 53.94377
> mean(tmp5)
[1] 73.33466
> Sum(tmp5)
[1] 14666.93
> Var(tmp5)
[1] 858.2148
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 89.64471 71.08924 73.87383 70.89531 71.12468 71.88359 71.70647 71.77919
[9] 69.02807 72.32146
> rowSums(tmp5)
[1] 1792.894 1421.785 1477.477 1417.906 1422.494 1437.672 1434.129 1435.584
[9] 1380.561 1446.429
> rowVars(tmp5)
[1] 7919.87871 99.42109 50.31935 106.33206 117.93875 100.66215
[7] 41.22212 61.63425 56.49156 109.57674
> rowSd(tmp5)
[1] 88.993700 9.971012 7.093614 10.311744 10.859961 10.033053 6.420446
[8] 7.850748 7.516086 10.467891
> rowMax(tmp5)
[1] 465.83756 89.03236 90.41159 90.73675 91.46194 89.76328 82.08674
[8] 85.70907 79.09608 94.68055
> rowMin(tmp5)
[1] 55.30491 55.42929 61.78868 55.99682 54.86587 56.78011 58.40987 53.94377
[9] 54.78840 55.23638
>
> colMeans(tmp5)
[1] 111.03668 72.70348 74.36392 70.83974 72.84011 75.34654 72.04570
[8] 70.60549 71.89915 71.82795 64.56367 72.08102 68.84239 70.03783
[15] 70.88093 68.59527 72.79820 74.51953 70.87257 69.99297
> colSums(tmp5)
[1] 1110.3668 727.0348 743.6392 708.3974 728.4011 753.4654 720.4570
[8] 706.0549 718.9915 718.2795 645.6367 720.8102 688.4239 700.3783
[15] 708.8093 685.9527 727.9820 745.1953 708.7257 699.9297
> colVars(tmp5)
[1] 15637.31649 65.98618 109.33185 74.60909 123.94871 98.42294
[7] 107.35901 86.82598 32.02013 91.24866 62.08894 83.13646
[13] 107.15470 90.56328 39.45439 81.47579 47.42862 80.61562
[19] 38.80618 136.27541
> colSd(tmp5)
[1] 125.049256 8.123188 10.456187 8.637655 11.133226 9.920834
[7] 10.361419 9.318046 5.658633 9.552416 7.879654 9.117920
[13] 10.351555 9.516474 6.281273 9.026394 6.886844 8.978620
[19] 6.229460 11.673706
> colMax(tmp5)
[1] 465.83756 89.76328 94.68055 81.76531 89.03236 88.10284 84.23032
[8] 87.33217 81.00167 85.24873 78.66483 90.41159 82.36628 91.46194
[15] 79.97906 82.57014 80.97847 90.73675 77.32370 92.63272
> colMin(tmp5)
[1] 57.10199 61.78868 61.61123 61.34570 54.78840 57.52270 55.23638 56.78011
[9] 64.83660 55.42929 55.30265 60.68537 53.94377 59.74930 62.62137 58.40987
[17] 60.54311 62.86896 55.99682 56.32177
>
>
> ### 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] 89.64471 71.08924 73.87383 NA 71.12468 71.88359 71.70647 71.77919
[9] 69.02807 72.32146
> rowSums(tmp5)
[1] 1792.894 1421.785 1477.477 NA 1422.494 1437.672 1434.129 1435.584
[9] 1380.561 1446.429
> rowVars(tmp5)
[1] 7919.87871 99.42109 50.31935 109.96316 117.93875 100.66215
[7] 41.22212 61.63425 56.49156 109.57674
> rowSd(tmp5)
[1] 88.993700 9.971012 7.093614 10.486332 10.859961 10.033053 6.420446
[8] 7.850748 7.516086 10.467891
> rowMax(tmp5)
[1] 465.83756 89.03236 90.41159 NA 91.46194 89.76328 82.08674
[8] 85.70907 79.09608 94.68055
> rowMin(tmp5)
[1] 55.30491 55.42929 61.78868 NA 54.86587 56.78011 58.40987 53.94377
[9] 54.78840 55.23638
>
> colMeans(tmp5)
[1] 111.03668 72.70348 74.36392 70.83974 72.84011 NA 72.04570
[8] 70.60549 71.89915 71.82795 64.56367 72.08102 68.84239 70.03783
[15] 70.88093 68.59527 72.79820 74.51953 70.87257 69.99297
> colSums(tmp5)
[1] 1110.3668 727.0348 743.6392 708.3974 728.4011 NA 720.4570
[8] 706.0549 718.9915 718.2795 645.6367 720.8102 688.4239 700.3783
[15] 708.8093 685.9527 727.9820 745.1953 708.7257 699.9297
> colVars(tmp5)
[1] 15637.31649 65.98618 109.33185 74.60909 123.94871 NA
[7] 107.35901 86.82598 32.02013 91.24866 62.08894 83.13646
[13] 107.15470 90.56328 39.45439 81.47579 47.42862 80.61562
[19] 38.80618 136.27541
> colSd(tmp5)
[1] 125.049256 8.123188 10.456187 8.637655 11.133226 NA
[7] 10.361419 9.318046 5.658633 9.552416 7.879654 9.117920
[13] 10.351555 9.516474 6.281273 9.026394 6.886844 8.978620
[19] 6.229460 11.673706
> colMax(tmp5)
[1] 465.83756 89.76328 94.68055 81.76531 89.03236 NA 84.23032
[8] 87.33217 81.00167 85.24873 78.66483 90.41159 82.36628 91.46194
[15] 79.97906 82.57014 80.97847 90.73675 77.32370 92.63272
> colMin(tmp5)
[1] 57.10199 61.78868 61.61123 61.34570 54.78840 NA 55.23638 56.78011
[9] 64.83660 55.42929 55.30265 60.68537 53.94377 59.74930 62.62137 58.40987
[17] 60.54311 62.86896 55.99682 56.32177
>
> Max(tmp5,na.rm=TRUE)
[1] 465.8376
> Min(tmp5,na.rm=TRUE)
[1] 53.94377
> mean(tmp5,na.rm=TRUE)
[1] 73.37826
> Sum(tmp5,na.rm=TRUE)
[1] 14602.27
> Var(tmp5,na.rm=TRUE)
[1] 862.1669
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 89.64471 71.08924 73.87383 71.22368 71.12468 71.88359 71.70647 71.77919
[9] 69.02807 72.32146
> rowSums(tmp5,na.rm=TRUE)
[1] 1792.894 1421.785 1477.477 1353.250 1422.494 1437.672 1434.129 1435.584
[9] 1380.561 1446.429
> rowVars(tmp5,na.rm=TRUE)
[1] 7919.87871 99.42109 50.31935 109.96316 117.93875 100.66215
[7] 41.22212 61.63425 56.49156 109.57674
> rowSd(tmp5,na.rm=TRUE)
[1] 88.993700 9.971012 7.093614 10.486332 10.859961 10.033053 6.420446
[8] 7.850748 7.516086 10.467891
> rowMax(tmp5,na.rm=TRUE)
[1] 465.83756 89.03236 90.41159 90.73675 91.46194 89.76328 82.08674
[8] 85.70907 79.09608 94.68055
> rowMin(tmp5,na.rm=TRUE)
[1] 55.30491 55.42929 61.78868 55.99682 54.86587 56.78011 58.40987 53.94377
[9] 54.78840 55.23638
>
> colMeans(tmp5,na.rm=TRUE)
[1] 111.03668 72.70348 74.36392 70.83974 72.84011 76.53433 72.04570
[8] 70.60549 71.89915 71.82795 64.56367 72.08102 68.84239 70.03783
[15] 70.88093 68.59527 72.79820 74.51953 70.87257 69.99297
> colSums(tmp5,na.rm=TRUE)
[1] 1110.3668 727.0348 743.6392 708.3974 728.4011 688.8089 720.4570
[8] 706.0549 718.9915 718.2795 645.6367 720.8102 688.4239 700.3783
[15] 708.8093 685.9527 727.9820 745.1953 708.7257 699.9297
> colVars(tmp5,na.rm=TRUE)
[1] 15637.31649 65.98618 109.33185 74.60909 123.94871 94.85382
[7] 107.35901 86.82598 32.02013 91.24866 62.08894 83.13646
[13] 107.15470 90.56328 39.45439 81.47579 47.42862 80.61562
[19] 38.80618 136.27541
> colSd(tmp5,na.rm=TRUE)
[1] 125.049256 8.123188 10.456187 8.637655 11.133226 9.739293
[7] 10.361419 9.318046 5.658633 9.552416 7.879654 9.117920
[13] 10.351555 9.516474 6.281273 9.026394 6.886844 8.978620
[19] 6.229460 11.673706
> colMax(tmp5,na.rm=TRUE)
[1] 465.83756 89.76328 94.68055 81.76531 89.03236 88.10284 84.23032
[8] 87.33217 81.00167 85.24873 78.66483 90.41159 82.36628 91.46194
[15] 79.97906 82.57014 80.97847 90.73675 77.32370 92.63272
> colMin(tmp5,na.rm=TRUE)
[1] 57.10199 61.78868 61.61123 61.34570 54.78840 57.52270 55.23638 56.78011
[9] 64.83660 55.42929 55.30265 60.68537 53.94377 59.74930 62.62137 58.40987
[17] 60.54311 62.86896 55.99682 56.32177
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 89.64471 71.08924 73.87383 NaN 71.12468 71.88359 71.70647 71.77919
[9] 69.02807 72.32146
> rowSums(tmp5,na.rm=TRUE)
[1] 1792.894 1421.785 1477.477 0.000 1422.494 1437.672 1434.129 1435.584
[9] 1380.561 1446.429
> rowVars(tmp5,na.rm=TRUE)
[1] 7919.87871 99.42109 50.31935 NA 117.93875 100.66215
[7] 41.22212 61.63425 56.49156 109.57674
> rowSd(tmp5,na.rm=TRUE)
[1] 88.993700 9.971012 7.093614 NA 10.859961 10.033053 6.420446
[8] 7.850748 7.516086 10.467891
> rowMax(tmp5,na.rm=TRUE)
[1] 465.83756 89.03236 90.41159 NA 91.46194 89.76328 82.08674
[8] 85.70907 79.09608 94.68055
> rowMin(tmp5,na.rm=TRUE)
[1] 55.30491 55.42929 61.78868 NA 54.86587 56.78011 58.40987 53.94377
[9] 54.78840 55.23638
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 116.74661 72.77342 72.67997 71.66167 72.27604 NaN 72.15207
[8] 68.74697 72.15916 71.46440 63.71979 73.21780 68.82659 71.08994
[15] 71.73481 67.04251 74.15988 72.71761 72.52543 69.88489
> colSums(tmp5,na.rm=TRUE)
[1] 1050.7195 654.9607 654.1198 644.9550 650.4843 0.0000 649.3686
[8] 618.7227 649.4324 643.1796 573.4781 658.9602 619.4394 639.8094
[15] 645.6133 603.3826 667.4389 654.4585 652.7288 628.9640
> colVars(tmp5,na.rm=TRUE)
[1] 17225.19374 74.17942 91.09709 76.33507 135.86278 NA
[7] 120.65159 58.82062 35.26208 101.16783 61.83868 78.99031
[13] 120.54623 89.43071 36.18379 64.53569 32.49786 54.16504
[19] 12.92252 153.17841
> colSd(tmp5,na.rm=TRUE)
[1] 131.244786 8.612748 9.544480 8.736994 11.656019 NA
[7] 10.984152 7.669460 5.938188 10.058222 7.863757 8.887649
[13] 10.979355 9.456781 6.015296 8.033411 5.700690 7.359690
[19] 3.594791 12.376527
> colMax(tmp5,na.rm=TRUE)
[1] 465.83756 89.76328 94.68055 81.76531 89.03236 -Inf 84.23032
[8] 79.78743 81.00167 85.24873 78.66483 90.41159 82.36628 91.46194
[15] 79.97906 81.56857 80.97847 82.63430 77.32370 92.63272
> colMin(tmp5,na.rm=TRUE)
[1] 57.10199 61.78868 61.61123 61.34570 54.78840 Inf 55.23638 56.78011
[9] 64.83660 55.42929 55.30265 60.68537 53.94377 59.74930 62.62137 58.40987
[17] 62.97142 62.86896 67.92417 56.32177
>
>
>
>
> 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] 140.5966 276.9639 264.2940 232.8761 357.6685 212.0904 280.6736 178.7928
[9] 228.6419 268.3343
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 140.5966 276.9639 264.2940 232.8761 357.6685 212.0904 280.6736 178.7928
[9] 228.6419 268.3343
>
>
>
> 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] -2.842171e-14 -1.136868e-13 -2.273737e-13 0.000000e+00 0.000000e+00
[6] -5.684342e-14 1.421085e-14 -1.705303e-13 1.136868e-13 2.842171e-14
[11] -2.842171e-14 0.000000e+00 4.263256e-14 1.136868e-13 5.684342e-14
[16] -1.136868e-13 -8.526513e-14 0.000000e+00 -2.842171e-14 7.105427e-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)
+ }
7 6
9 12
10 6
7 3
10 19
10 18
2 20
9 12
5 4
7 20
5 11
4 14
4 10
6 7
7 3
8 8
6 9
10 11
7 11
1 10
There were 50 or more warnings (use warnings() to see the first 50)
>
>
> ### now test 1 by n and n by 1 matrix
>
>
> err.tol <- 1e-12
>
> rm(tmp5)
>
> dataset1 <- rnorm(100)
> dataset2 <- rnorm(100)
>
> tmp <- createBufferedMatrix(1,100)
> tmp[1,] <- dataset1
>
> tmp2 <- createBufferedMatrix(100,1)
> tmp2[,1] <- dataset2
>
>
>
>
>
> Max(tmp)
[1] 2.11726
> Min(tmp)
[1] -2.537017
> mean(tmp)
[1] -0.1390517
> Sum(tmp)
[1] -13.90517
> Var(tmp)
[1] 0.9789614
>
> rowMeans(tmp)
[1] -0.1390517
> rowSums(tmp)
[1] -13.90517
> rowVars(tmp)
[1] 0.9789614
> rowSd(tmp)
[1] 0.9894248
> rowMax(tmp)
[1] 2.11726
> rowMin(tmp)
[1] -2.537017
>
> colMeans(tmp)
[1] 1.21824699 -0.03808557 -0.43288164 -2.53701698 -1.23421629 0.02870939
[7] -1.31309628 0.34530621 -0.83042004 -0.55324379 -0.38853175 1.80333848
[13] 0.48360578 0.23969864 -0.53128802 0.64540818 -0.16315619 -1.20820039
[19] -1.98979847 0.27827781 -0.91942305 1.13174668 -0.50379420 0.16717986
[25] 0.29823815 -0.97002485 -0.67736856 -1.26404213 0.69084303 2.11726033
[31] -1.50424019 -0.99272754 -0.91783777 -0.02395347 0.43538159 0.72481096
[37] -1.31449359 0.41348879 1.37987472 -0.38583795 -0.43196580 -0.19473718
[43] 1.97030021 -1.05836767 0.95428758 -0.46176082 -1.28760221 -0.49051749
[49] 0.09176308 -0.49365447 1.63132970 -1.91714284 -1.78719929 -0.37036127
[55] 1.55939448 1.27870631 0.94160588 -0.16475688 -1.95263961 -0.29384580
[61] 0.10680511 -0.57092058 0.23904438 0.37194628 -1.25278644 -0.06226850
[67] 0.34310740 -0.62675776 -0.29540355 1.19833196 -0.93664436 0.58895486
[73] 0.82890663 0.54386042 -0.19465729 -0.92849351 0.66705501 -0.05649988
[79] 0.80418810 0.77286691 -0.75215839 1.44260725 -0.30320066 0.89875124
[85] 0.47414829 0.26991757 -0.83434839 -0.36969821 -0.77769482 -0.12563918
[91] -2.08125179 -0.67407216 -1.77542241 0.69659017 -1.27951411 1.60914909
[97] -0.42885009 0.25921173 -1.61025060 0.68534355
> colSums(tmp)
[1] 1.21824699 -0.03808557 -0.43288164 -2.53701698 -1.23421629 0.02870939
[7] -1.31309628 0.34530621 -0.83042004 -0.55324379 -0.38853175 1.80333848
[13] 0.48360578 0.23969864 -0.53128802 0.64540818 -0.16315619 -1.20820039
[19] -1.98979847 0.27827781 -0.91942305 1.13174668 -0.50379420 0.16717986
[25] 0.29823815 -0.97002485 -0.67736856 -1.26404213 0.69084303 2.11726033
[31] -1.50424019 -0.99272754 -0.91783777 -0.02395347 0.43538159 0.72481096
[37] -1.31449359 0.41348879 1.37987472 -0.38583795 -0.43196580 -0.19473718
[43] 1.97030021 -1.05836767 0.95428758 -0.46176082 -1.28760221 -0.49051749
[49] 0.09176308 -0.49365447 1.63132970 -1.91714284 -1.78719929 -0.37036127
[55] 1.55939448 1.27870631 0.94160588 -0.16475688 -1.95263961 -0.29384580
[61] 0.10680511 -0.57092058 0.23904438 0.37194628 -1.25278644 -0.06226850
[67] 0.34310740 -0.62675776 -0.29540355 1.19833196 -0.93664436 0.58895486
[73] 0.82890663 0.54386042 -0.19465729 -0.92849351 0.66705501 -0.05649988
[79] 0.80418810 0.77286691 -0.75215839 1.44260725 -0.30320066 0.89875124
[85] 0.47414829 0.26991757 -0.83434839 -0.36969821 -0.77769482 -0.12563918
[91] -2.08125179 -0.67407216 -1.77542241 0.69659017 -1.27951411 1.60914909
[97] -0.42885009 0.25921173 -1.61025060 0.68534355
> 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] 1.21824699 -0.03808557 -0.43288164 -2.53701698 -1.23421629 0.02870939
[7] -1.31309628 0.34530621 -0.83042004 -0.55324379 -0.38853175 1.80333848
[13] 0.48360578 0.23969864 -0.53128802 0.64540818 -0.16315619 -1.20820039
[19] -1.98979847 0.27827781 -0.91942305 1.13174668 -0.50379420 0.16717986
[25] 0.29823815 -0.97002485 -0.67736856 -1.26404213 0.69084303 2.11726033
[31] -1.50424019 -0.99272754 -0.91783777 -0.02395347 0.43538159 0.72481096
[37] -1.31449359 0.41348879 1.37987472 -0.38583795 -0.43196580 -0.19473718
[43] 1.97030021 -1.05836767 0.95428758 -0.46176082 -1.28760221 -0.49051749
[49] 0.09176308 -0.49365447 1.63132970 -1.91714284 -1.78719929 -0.37036127
[55] 1.55939448 1.27870631 0.94160588 -0.16475688 -1.95263961 -0.29384580
[61] 0.10680511 -0.57092058 0.23904438 0.37194628 -1.25278644 -0.06226850
[67] 0.34310740 -0.62675776 -0.29540355 1.19833196 -0.93664436 0.58895486
[73] 0.82890663 0.54386042 -0.19465729 -0.92849351 0.66705501 -0.05649988
[79] 0.80418810 0.77286691 -0.75215839 1.44260725 -0.30320066 0.89875124
[85] 0.47414829 0.26991757 -0.83434839 -0.36969821 -0.77769482 -0.12563918
[91] -2.08125179 -0.67407216 -1.77542241 0.69659017 -1.27951411 1.60914909
[97] -0.42885009 0.25921173 -1.61025060 0.68534355
> colMin(tmp)
[1] 1.21824699 -0.03808557 -0.43288164 -2.53701698 -1.23421629 0.02870939
[7] -1.31309628 0.34530621 -0.83042004 -0.55324379 -0.38853175 1.80333848
[13] 0.48360578 0.23969864 -0.53128802 0.64540818 -0.16315619 -1.20820039
[19] -1.98979847 0.27827781 -0.91942305 1.13174668 -0.50379420 0.16717986
[25] 0.29823815 -0.97002485 -0.67736856 -1.26404213 0.69084303 2.11726033
[31] -1.50424019 -0.99272754 -0.91783777 -0.02395347 0.43538159 0.72481096
[37] -1.31449359 0.41348879 1.37987472 -0.38583795 -0.43196580 -0.19473718
[43] 1.97030021 -1.05836767 0.95428758 -0.46176082 -1.28760221 -0.49051749
[49] 0.09176308 -0.49365447 1.63132970 -1.91714284 -1.78719929 -0.37036127
[55] 1.55939448 1.27870631 0.94160588 -0.16475688 -1.95263961 -0.29384580
[61] 0.10680511 -0.57092058 0.23904438 0.37194628 -1.25278644 -0.06226850
[67] 0.34310740 -0.62675776 -0.29540355 1.19833196 -0.93664436 0.58895486
[73] 0.82890663 0.54386042 -0.19465729 -0.92849351 0.66705501 -0.05649988
[79] 0.80418810 0.77286691 -0.75215839 1.44260725 -0.30320066 0.89875124
[85] 0.47414829 0.26991757 -0.83434839 -0.36969821 -0.77769482 -0.12563918
[91] -2.08125179 -0.67407216 -1.77542241 0.69659017 -1.27951411 1.60914909
[97] -0.42885009 0.25921173 -1.61025060 0.68534355
> colMedians(tmp)
[1] 1.21824699 -0.03808557 -0.43288164 -2.53701698 -1.23421629 0.02870939
[7] -1.31309628 0.34530621 -0.83042004 -0.55324379 -0.38853175 1.80333848
[13] 0.48360578 0.23969864 -0.53128802 0.64540818 -0.16315619 -1.20820039
[19] -1.98979847 0.27827781 -0.91942305 1.13174668 -0.50379420 0.16717986
[25] 0.29823815 -0.97002485 -0.67736856 -1.26404213 0.69084303 2.11726033
[31] -1.50424019 -0.99272754 -0.91783777 -0.02395347 0.43538159 0.72481096
[37] -1.31449359 0.41348879 1.37987472 -0.38583795 -0.43196580 -0.19473718
[43] 1.97030021 -1.05836767 0.95428758 -0.46176082 -1.28760221 -0.49051749
[49] 0.09176308 -0.49365447 1.63132970 -1.91714284 -1.78719929 -0.37036127
[55] 1.55939448 1.27870631 0.94160588 -0.16475688 -1.95263961 -0.29384580
[61] 0.10680511 -0.57092058 0.23904438 0.37194628 -1.25278644 -0.06226850
[67] 0.34310740 -0.62675776 -0.29540355 1.19833196 -0.93664436 0.58895486
[73] 0.82890663 0.54386042 -0.19465729 -0.92849351 0.66705501 -0.05649988
[79] 0.80418810 0.77286691 -0.75215839 1.44260725 -0.30320066 0.89875124
[85] 0.47414829 0.26991757 -0.83434839 -0.36969821 -0.77769482 -0.12563918
[91] -2.08125179 -0.67407216 -1.77542241 0.69659017 -1.27951411 1.60914909
[97] -0.42885009 0.25921173 -1.61025060 0.68534355
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] 1.218247 -0.03808557 -0.4328816 -2.537017 -1.234216 0.02870939 -1.313096
[2,] 1.218247 -0.03808557 -0.4328816 -2.537017 -1.234216 0.02870939 -1.313096
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] 0.3453062 -0.83042 -0.5532438 -0.3885318 1.803338 0.4836058 0.2396986
[2,] 0.3453062 -0.83042 -0.5532438 -0.3885318 1.803338 0.4836058 0.2396986
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] -0.531288 0.6454082 -0.1631562 -1.2082 -1.989798 0.2782778 -0.9194231
[2,] -0.531288 0.6454082 -0.1631562 -1.2082 -1.989798 0.2782778 -0.9194231
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] 1.131747 -0.5037942 0.1671799 0.2982381 -0.9700248 -0.6773686 -1.264042
[2,] 1.131747 -0.5037942 0.1671799 0.2982381 -0.9700248 -0.6773686 -1.264042
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] 0.690843 2.11726 -1.50424 -0.9927275 -0.9178378 -0.02395347 0.4353816
[2,] 0.690843 2.11726 -1.50424 -0.9927275 -0.9178378 -0.02395347 0.4353816
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] 0.724811 -1.314494 0.4134888 1.379875 -0.385838 -0.4319658 -0.1947372
[2,] 0.724811 -1.314494 0.4134888 1.379875 -0.385838 -0.4319658 -0.1947372
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] 1.9703 -1.058368 0.9542876 -0.4617608 -1.287602 -0.4905175 0.09176308
[2,] 1.9703 -1.058368 0.9542876 -0.4617608 -1.287602 -0.4905175 0.09176308
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] -0.4936545 1.63133 -1.917143 -1.787199 -0.3703613 1.559394 1.278706
[2,] -0.4936545 1.63133 -1.917143 -1.787199 -0.3703613 1.559394 1.278706
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] 0.9416059 -0.1647569 -1.95264 -0.2938458 0.1068051 -0.5709206 0.2390444
[2,] 0.9416059 -0.1647569 -1.95264 -0.2938458 0.1068051 -0.5709206 0.2390444
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] 0.3719463 -1.252786 -0.0622685 0.3431074 -0.6267578 -0.2954035 1.198332
[2,] 0.3719463 -1.252786 -0.0622685 0.3431074 -0.6267578 -0.2954035 1.198332
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] -0.9366444 0.5889549 0.8289066 0.5438604 -0.1946573 -0.9284935 0.667055
[2,] -0.9366444 0.5889549 0.8289066 0.5438604 -0.1946573 -0.9284935 0.667055
[,78] [,79] [,80] [,81] [,82] [,83] [,84]
[1,] -0.05649988 0.8041881 0.7728669 -0.7521584 1.442607 -0.3032007 0.8987512
[2,] -0.05649988 0.8041881 0.7728669 -0.7521584 1.442607 -0.3032007 0.8987512
[,85] [,86] [,87] [,88] [,89] [,90] [,91]
[1,] 0.4741483 0.2699176 -0.8343484 -0.3696982 -0.7776948 -0.1256392 -2.081252
[2,] 0.4741483 0.2699176 -0.8343484 -0.3696982 -0.7776948 -0.1256392 -2.081252
[,92] [,93] [,94] [,95] [,96] [,97] [,98]
[1,] -0.6740722 -1.775422 0.6965902 -1.279514 1.609149 -0.4288501 0.2592117
[2,] -0.6740722 -1.775422 0.6965902 -1.279514 1.609149 -0.4288501 0.2592117
[,99] [,100]
[1,] -1.610251 0.6853436
[2,] -1.610251 0.6853436
>
>
> Max(tmp2)
[1] 2.213965
> Min(tmp2)
[1] -2.764388
> mean(tmp2)
[1] 0.03008202
> Sum(tmp2)
[1] 3.008202
> Var(tmp2)
[1] 0.917878
>
> rowMeans(tmp2)
[1] 0.07399179 0.51057297 0.13068284 -0.02054116 0.56280693 1.52352403
[7] -0.18281734 2.02269039 0.44046588 0.36835618 -0.29144755 1.66570540
[13] 0.91311931 0.42419083 -0.25473451 -0.68395895 0.35534212 0.23564934
[19] -0.42438367 0.11258384 -1.57827761 1.57866143 1.68267707 0.45906931
[25] 0.02523859 1.33666360 -0.43098031 -1.39452753 -0.38571876 -0.01922740
[31] -0.71828948 0.95929558 0.08874924 0.74865654 -0.20433037 -1.82769078
[37] 1.25976357 0.79347833 -0.34648894 -0.73786590 1.12408722 -0.42892414
[43] -0.86128337 0.19448716 -0.39107555 -0.25143180 -0.62182214 -0.15098722
[49] -0.99803146 -0.70025461 0.19235814 0.35145896 0.60284279 0.46534742
[55] -1.65101347 -0.61950451 0.46997925 1.49329261 1.51946056 0.21060563
[61] -0.40232325 -2.27162213 2.21396536 -2.32010353 0.23961380 0.28338481
[67] 1.07963640 -0.61433661 0.28290937 -0.09734051 0.05661366 1.02776199
[73] -1.50152008 -2.76438783 -0.20104377 -1.67448712 -0.18867188 0.45700715
[79] -1.21706172 0.06610607 -0.65772442 0.52523673 0.40698067 0.89732387
[85] -0.06228578 0.86037537 1.04485279 0.50612588 -0.91069218 -0.21933491
[91] 1.06906936 0.94386485 -0.96870015 -0.51310183 -0.07208393 0.69385755
[97] 0.37713218 -0.63759698 -1.85904988 0.40960584
> rowSums(tmp2)
[1] 0.07399179 0.51057297 0.13068284 -0.02054116 0.56280693 1.52352403
[7] -0.18281734 2.02269039 0.44046588 0.36835618 -0.29144755 1.66570540
[13] 0.91311931 0.42419083 -0.25473451 -0.68395895 0.35534212 0.23564934
[19] -0.42438367 0.11258384 -1.57827761 1.57866143 1.68267707 0.45906931
[25] 0.02523859 1.33666360 -0.43098031 -1.39452753 -0.38571876 -0.01922740
[31] -0.71828948 0.95929558 0.08874924 0.74865654 -0.20433037 -1.82769078
[37] 1.25976357 0.79347833 -0.34648894 -0.73786590 1.12408722 -0.42892414
[43] -0.86128337 0.19448716 -0.39107555 -0.25143180 -0.62182214 -0.15098722
[49] -0.99803146 -0.70025461 0.19235814 0.35145896 0.60284279 0.46534742
[55] -1.65101347 -0.61950451 0.46997925 1.49329261 1.51946056 0.21060563
[61] -0.40232325 -2.27162213 2.21396536 -2.32010353 0.23961380 0.28338481
[67] 1.07963640 -0.61433661 0.28290937 -0.09734051 0.05661366 1.02776199
[73] -1.50152008 -2.76438783 -0.20104377 -1.67448712 -0.18867188 0.45700715
[79] -1.21706172 0.06610607 -0.65772442 0.52523673 0.40698067 0.89732387
[85] -0.06228578 0.86037537 1.04485279 0.50612588 -0.91069218 -0.21933491
[91] 1.06906936 0.94386485 -0.96870015 -0.51310183 -0.07208393 0.69385755
[97] 0.37713218 -0.63759698 -1.85904988 0.40960584
> 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] 0.07399179 0.51057297 0.13068284 -0.02054116 0.56280693 1.52352403
[7] -0.18281734 2.02269039 0.44046588 0.36835618 -0.29144755 1.66570540
[13] 0.91311931 0.42419083 -0.25473451 -0.68395895 0.35534212 0.23564934
[19] -0.42438367 0.11258384 -1.57827761 1.57866143 1.68267707 0.45906931
[25] 0.02523859 1.33666360 -0.43098031 -1.39452753 -0.38571876 -0.01922740
[31] -0.71828948 0.95929558 0.08874924 0.74865654 -0.20433037 -1.82769078
[37] 1.25976357 0.79347833 -0.34648894 -0.73786590 1.12408722 -0.42892414
[43] -0.86128337 0.19448716 -0.39107555 -0.25143180 -0.62182214 -0.15098722
[49] -0.99803146 -0.70025461 0.19235814 0.35145896 0.60284279 0.46534742
[55] -1.65101347 -0.61950451 0.46997925 1.49329261 1.51946056 0.21060563
[61] -0.40232325 -2.27162213 2.21396536 -2.32010353 0.23961380 0.28338481
[67] 1.07963640 -0.61433661 0.28290937 -0.09734051 0.05661366 1.02776199
[73] -1.50152008 -2.76438783 -0.20104377 -1.67448712 -0.18867188 0.45700715
[79] -1.21706172 0.06610607 -0.65772442 0.52523673 0.40698067 0.89732387
[85] -0.06228578 0.86037537 1.04485279 0.50612588 -0.91069218 -0.21933491
[91] 1.06906936 0.94386485 -0.96870015 -0.51310183 -0.07208393 0.69385755
[97] 0.37713218 -0.63759698 -1.85904988 0.40960584
> rowMin(tmp2)
[1] 0.07399179 0.51057297 0.13068284 -0.02054116 0.56280693 1.52352403
[7] -0.18281734 2.02269039 0.44046588 0.36835618 -0.29144755 1.66570540
[13] 0.91311931 0.42419083 -0.25473451 -0.68395895 0.35534212 0.23564934
[19] -0.42438367 0.11258384 -1.57827761 1.57866143 1.68267707 0.45906931
[25] 0.02523859 1.33666360 -0.43098031 -1.39452753 -0.38571876 -0.01922740
[31] -0.71828948 0.95929558 0.08874924 0.74865654 -0.20433037 -1.82769078
[37] 1.25976357 0.79347833 -0.34648894 -0.73786590 1.12408722 -0.42892414
[43] -0.86128337 0.19448716 -0.39107555 -0.25143180 -0.62182214 -0.15098722
[49] -0.99803146 -0.70025461 0.19235814 0.35145896 0.60284279 0.46534742
[55] -1.65101347 -0.61950451 0.46997925 1.49329261 1.51946056 0.21060563
[61] -0.40232325 -2.27162213 2.21396536 -2.32010353 0.23961380 0.28338481
[67] 1.07963640 -0.61433661 0.28290937 -0.09734051 0.05661366 1.02776199
[73] -1.50152008 -2.76438783 -0.20104377 -1.67448712 -0.18867188 0.45700715
[79] -1.21706172 0.06610607 -0.65772442 0.52523673 0.40698067 0.89732387
[85] -0.06228578 0.86037537 1.04485279 0.50612588 -0.91069218 -0.21933491
[91] 1.06906936 0.94386485 -0.96870015 -0.51310183 -0.07208393 0.69385755
[97] 0.37713218 -0.63759698 -1.85904988 0.40960584
>
> colMeans(tmp2)
[1] 0.03008202
> colSums(tmp2)
[1] 3.008202
> colVars(tmp2)
[1] 0.917878
> colSd(tmp2)
[1] 0.9580595
> colMax(tmp2)
[1] 2.213965
> colMin(tmp2)
[1] -2.764388
> colMedians(tmp2)
[1] 0.08137051
> colRanges(tmp2)
[,1]
[1,] -2.764388
[2,] 2.213965
>
> 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] -5.515636 2.029454 3.445461 4.296857 2.595870 4.383454 -1.097726
[8] -5.057536 -2.016501 1.715753
> colApply(tmp,quantile)[,1]
[,1]
[1,] -2.19917094
[2,] -0.87217007
[3,] -0.66794314
[4,] -0.09446276
[5,] 0.94595409
>
> rowApply(tmp,sum)
[1] 1.9983726 2.5444896 -1.0546627 -1.0164194 2.1929094 -5.6081024
[7] -2.1474727 5.6204731 0.1311986 2.1186644
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 5 2 5 1 3 2 6 8 3
[2,] 5 7 4 10 3 4 10 5 2 2
[3,] 9 9 3 9 9 10 1 10 7 8
[4,] 6 8 10 6 5 5 7 7 6 4
[5,] 10 1 6 3 6 6 6 4 3 9
[6,] 3 3 5 8 8 8 9 9 1 10
[7,] 8 2 9 2 2 9 3 3 4 5
[8,] 4 4 7 1 4 1 4 2 9 7
[9,] 7 6 1 4 10 2 8 1 5 6
[10,] 2 10 8 7 7 7 5 8 10 1
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] 5.27642341 0.64423163 1.81662451 0.84003415 -2.79297112 -0.02556821
[7] -1.36250751 4.37345237 0.14672556 3.06096814 -0.01299772 -3.16101510
[13] -0.43759574 -1.82217930 1.97944786 -0.66805249 2.36331422 -2.57085582
[19] -0.85633135 -3.25417875
> colApply(tmp,quantile)[,1]
[,1]
[1,] 0.2831857
[2,] 0.4781712
[3,] 1.2220983
[4,] 1.4226938
[5,] 1.8702744
>
> rowApply(tmp,sum)
[1] 8.226585 1.290783 -7.478229 -5.053892 6.551721
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 16 19 17 13 18
[2,] 19 2 5 11 19
[3,] 8 20 14 15 3
[4,] 17 3 6 19 10
[5,] 7 6 13 1 8
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 1.2220983 1.6983202 0.23728233 1.2323185 0.18655536 -0.1532526
[2,] 1.8702744 -1.3945330 2.06492266 -0.9808119 -0.72008269 0.7161771
[3,] 0.4781712 -0.9550042 -0.01984464 -0.9516585 -0.07931132 -0.3050951
[4,] 0.2831857 -0.1969221 0.46104062 1.1471288 -2.34971695 -0.7686847
[5,] 1.4226938 1.4923708 -0.92677645 0.3930573 0.16958448 0.4852871
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] -1.0937117 1.4406680 1.1591100 1.9910598 0.7270104 -1.5766006
[2,] -0.2616150 0.6265946 -1.7017196 0.6893268 -0.9428709 -0.8490446
[3,] 0.5243770 0.3241810 -0.6421990 1.0560382 -1.9910125 -0.4525684
[4,] -0.8143890 -0.5898098 0.8356777 -1.5070641 1.5503788 -1.0624187
[5,] 0.2828312 2.5718187 0.4958565 0.8316075 0.6434965 0.7796172
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] 0.5410215 0.9080068 -0.2361601 0.42470890 0.6125116 0.3873116
[2,] 0.3275674 -0.3377630 1.5494405 0.42062714 1.1034229 0.2764507
[3,] -0.5669887 -1.7041277 1.2288371 -1.48276348 0.2265230 -0.7644692
[4,] -1.2102328 -0.2537477 0.4732102 -0.01239590 0.3484456 -1.9796729
[5,] 0.4710368 -0.4345477 -1.0358797 -0.01822915 0.0724111 -0.4904760
[,19] [,20]
[1,] -0.6958621 -0.7858107
[2,] -0.6241450 -0.5414349
[3,] -1.0348595 -0.3664543
[4,] 1.0617112 -0.4696159
[5,] 0.4368241 -1.0908630
>
>
> is.BufferedMatrix(tmp)
[1] TRUE
>
> as.BufferedMatrix(as.matrix(tmp))
BufferedMatrix object
Matrix size: 5 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 800 bytes.
>
>
>
> subBufferedMatrix(tmp,1:5,1:5)
BufferedMatrix object
Matrix size: 5 5
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 653 bytes.
Disk usage : 200 bytes.
> subBufferedMatrix(tmp,,5:8)
BufferedMatrix object
Matrix size: 5 4
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 566 bytes.
Disk usage : 160 bytes.
> subBufferedMatrix(tmp,1:3,)
BufferedMatrix object
Matrix size: 3 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 480 bytes.
>
>
> rm(tmp)
>
>
> ###
> ### Testing colnames and rownames
> ###
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
>
>
> colnames(tmp)
NULL
> rownames(tmp)
NULL
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> colnames(tmp)
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
> rownames(tmp)
[1] "row1" "row2" "row3" "row4" "row5"
>
>
> tmp["row1",]
col1 col2 col3 col4 col5 col6 col7
row1 0.03319647 0.2204145 0.3814751 1.204008 0.3128905 0.209444 -0.2051207
col8 col9 col10 col11 col12 col13 col14
row1 -0.8784667 -0.3988287 1.137178 -0.588068 0.2507867 -1.047566 -0.7962906
col15 col16 col17 col18 col19 col20
row1 1.868071 0.4109912 -1.538502 1.796754 1.258647 -0.2709407
> tmp[,"col10"]
col10
row1 1.1371775
row2 0.2479280
row3 1.4510930
row4 -0.2924615
row5 0.6703627
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7
row1 0.03319647 0.2204145 0.3814751 1.2040081 0.3128905 0.209444 -0.2051207
row5 1.02314147 0.1811596 1.4252462 -0.3371317 0.2159131 0.689030 2.4363393
col8 col9 col10 col11 col12 col13 col14
row1 -0.8784667 -0.3988287 1.1371775 -0.5880680 0.2507867 -1.0475656 -0.7962906
row5 -0.2147631 1.4739363 0.6703627 -0.4017542 0.9772095 -0.4315068 -1.3467106
col15 col16 col17 col18 col19 col20
row1 1.868071 0.4109912 -1.538502 1.796754 1.258647 -0.2709407
row5 1.003525 -0.5711859 1.514960 -1.040821 2.017229 0.9460007
> tmp[,c("col6","col20")]
col6 col20
row1 0.2094440 -0.2709407
row2 0.9571521 -0.1056699
row3 -2.5195381 -1.4218508
row4 -2.0216493 -0.9379884
row5 0.6890300 0.9460007
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 0.209444 -0.2709407
row5 0.689030 0.9460007
>
>
>
>
> 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 49.79141 49.31912 49.97835 49.96089 49.34089 105.6703 50.19377 50.4829
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.15979 47.95423 48.81867 49.31683 50.33754 47.40864 51.04643 49.27531
col17 col18 col19 col20
row1 50.31596 48.32672 49.93805 105.1146
> tmp[,"col10"]
col10
row1 47.95423
row2 32.13697
row3 28.85684
row4 31.00306
row5 50.26666
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 49.79141 49.31912 49.97835 49.96089 49.34089 105.6703 50.19377 50.48290
row5 48.41631 51.33733 49.64526 50.38024 51.22891 104.6411 50.03477 52.43643
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.15979 47.95423 48.81867 49.31683 50.33754 47.40864 51.04643 49.27531
row5 51.83621 50.26666 48.66453 50.24252 49.69560 50.06161 48.25186 50.36180
col17 col18 col19 col20
row1 50.31596 48.32672 49.93805 105.1146
row5 50.43054 50.30805 49.06671 107.0839
> tmp[,c("col6","col20")]
col6 col20
row1 105.67034 105.11458
row2 75.24601 74.21500
row3 74.45647 73.20680
row4 75.31134 74.48997
row5 104.64106 107.08385
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 105.6703 105.1146
row5 104.6411 107.0839
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 105.6703 105.1146
row5 104.6411 107.0839
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] -0.3948211
[2,] -0.1406370
[3,] -1.3608895
[4,] 0.7416837
[5,] 0.2869800
> tmp[,c("col17","col7")]
col17 col7
[1,] -0.89324401 -1.1924299
[2,] 0.12414265 -0.2370256
[3,] 0.04471943 -0.4223647
[4,] -0.85558933 -0.5007229
[5,] -0.15566800 1.0520000
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] -1.2964619 -1.01322652
[2,] -0.4419108 -0.05768143
[3,] -1.2888593 -1.97089472
[4,] 3.9125946 1.05952183
[5,] -1.4672629 -1.55443400
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] -1.296462
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] -1.2964619
[2,] -0.4419108
>
>
>
> 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 0.3296696 -0.6528428 -1.1436317 -0.008538992 -1.1808454 0.9354066
row1 -0.2868078 -1.3055446 0.0544434 0.890608315 -0.4884151 -1.5478729
[,7] [,8] [,9] [,10] [,11] [,12] [,13]
row3 1.145111 1.6245015 0.4005559 0.7556419 0.1050430 -1.6265957 1.2665340
row1 -1.137795 -0.2450891 -0.2115491 0.8042087 0.6295545 -0.6539882 -0.1942415
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
row3 1.511471 0.116744 -1.5115477 -0.4669604 -0.5668274 -0.6767815 1.301691
row1 1.732987 1.656730 0.7439143 -0.6384071 -1.3463832 0.3459678 -1.204235
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 -1.478733 2.308771 0.1946739 0.2272829 0.5949617 0.2601708 0.1701366
[,8] [,9] [,10]
row2 -2.037549 0.6384802 0.2797291
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 1.221626 -0.9768914 0.0841396 1.538699 0.6416319 -0.1294674 1.173831
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 -1.162799 -0.8973627 -0.2258862 1.35606 0.0285823 0.6088504 -1.460232
[,15] [,16] [,17] [,18] [,19] [,20]
row5 0.04260224 0.04145353 1.438377 0.4644996 0.9549115 -1.091783
>
>
> 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: 0x620fcd4d6f10>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM299a99a97982c"
[2] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM299a9970ebc842"
[3] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM299a9956969d30"
[4] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM299a9944f42221"
[5] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM299a9953369ca6"
[6] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM299a997dac61d"
[7] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM299a991ea299de"
[8] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM299a995889d885"
[9] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM299a9933ae3f45"
[10] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM299a9939a64f1e"
[11] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM299a99257b5f44"
[12] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM299a99781cca24"
[13] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM299a99651b1522"
[14] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM299a992728cdd2"
[15] "/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests/BM299a993433a9ad"
>
>
> ### 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: 0x620fcd8d0110>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x620fcd8d0110>
Warning message:
In dir.create(new.directory) :
'/home/biocbuild/bbs-3.23-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x620fcd8d0110>
> rowMedians(tmp)
[1] -0.291247376 -0.349120994 0.110919905 0.231059456 -0.058643553
[6] -0.285001104 -0.101781019 -0.014628744 -0.113213482 0.013866655
[11] 0.196192122 0.028979515 0.156163266 -0.054121886 -0.142656561
[16] -0.032582982 0.720344010 0.101453843 -0.433019759 0.177660263
[21] -0.028834248 0.007270743 -0.256034769 -0.205173798 0.030383177
[26] -0.382183415 0.620374634 0.025976876 -0.012602545 -0.456130462
[31] -0.487620657 0.705744648 0.085867154 -0.074170185 0.145959164
[36] 0.130856064 0.544150135 0.193103135 -0.347260882 -0.660875316
[41] 0.617226414 0.361362522 0.259211227 -0.430833486 0.167012906
[46] -0.021218153 0.576583864 -0.310034046 -0.609820267 -0.010310528
[51] -0.020809170 0.155449370 0.435529922 -0.379520612 0.077207650
[56] 0.067571949 0.206296085 -0.749912150 0.213046341 0.054866048
[61] -0.466273726 -0.477046194 0.435340319 -0.148522237 0.249990160
[66] -0.934587086 -0.109831008 0.251872594 -0.455071877 -0.029641084
[71] 0.220791260 -0.061093832 0.108947081 -0.130714642 -0.187353872
[76] 0.018713238 0.052275972 -0.388429137 0.237850907 0.367302203
[81] 0.065112122 -0.172195186 -0.147750581 0.482448200 0.138135300
[86] -0.137864468 -0.437672527 -0.355383037 -0.414762864 -0.235148385
[91] 0.225979454 -0.274555334 0.268900189 -0.127698360 0.486527072
[96] 0.158756763 -0.036816464 -0.120748800 0.058061213 -0.035992237
[101] 0.075691795 -0.113177993 -0.204299946 0.505306605 0.096199400
[106] 0.333777883 0.127186381 0.461589468 -0.337005715 0.484209455
[111] 0.192339540 -0.582250830 -0.115185740 0.033425389 0.276697691
[116] -0.406212928 0.216705764 -0.025310650 0.226303109 -0.083149589
[121] 0.388068223 0.067844620 0.269472777 0.542643565 0.258375260
[126] 0.251326876 0.445324888 -0.054245416 -0.102717510 0.324499007
[131] -0.597700907 -0.389693027 -0.509166237 0.288142177 -0.210770304
[136] -0.275243825 0.442181103 -0.332224435 -0.313279352 -0.243879496
[141] 0.239449946 0.502610536 0.666776308 -0.076605562 -0.278687629
[146] 0.458600005 -0.356237117 -0.126657148 0.612895237 0.060250104
[151] -0.067316245 -0.079401920 0.221896729 -0.188938699 -0.131398780
[156] -0.034943272 0.189591112 -0.012044018 0.275455423 -0.360858306
[161] 0.141679328 -0.355098943 -0.159084703 -0.508197565 0.193894767
[166] 0.044997205 0.394603521 -0.308805571 0.027250392 -0.117736793
[171] -0.153129163 -0.199986319 -0.139751573 -0.275663522 0.405497717
[176] 0.223102186 -0.065489390 -0.077123951 0.575813198 0.156282316
[181] -0.035265489 -0.026888276 0.215433108 -0.098986377 -0.081857020
[186] 0.281170207 0.523792932 -0.221953439 -0.360348957 0.234577790
[191] 0.090781333 -0.010689672 -0.063464340 -0.376936566 -0.120487098
[196] 0.037906715 0.232489661 -0.324518760 0.106793960 0.055055336
[201] -0.430861436 0.008367661 0.106749743 -0.185064869 0.127280182
[206] 0.005858675 0.076785671 0.118440351 -0.107047400 -0.071411407
[211] 0.010571483 -0.221641256 -0.337899925 0.411533062 0.156307053
[216] -0.132628660 -0.347338563 0.486173007 -0.025247321 -0.246236945
[221] 0.378653301 -0.207264639 0.479527026 0.711703716 0.357721818
[226] 0.137077700 0.056873563 -0.439336002 0.501943105 -0.158233860
>
> proc.time()
user system elapsed
1.380 1.478 2.852
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
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: 0x62e22c6e2b20>
> .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: 0x62e22c6e2b20>
> .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: 0x62e22c6e2b20>
> .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: 0x62e22c6e2b20>
> 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: 0x62e22c6c3410>
> .Call("R_bm_AddColumn",P)
<pointer: 0x62e22c6c3410>
> .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: 0x62e22c6c3410>
> .Call("R_bm_AddColumn",P)
<pointer: 0x62e22c6c3410>
> .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: 0x62e22c6c3410>
> 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: 0x62e22af707a0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x62e22af707a0>
> .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: 0x62e22af707a0>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x62e22af707a0>
> .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: 0x62e22af707a0>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x62e22af707a0>
> .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: 0x62e22af707a0>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x62e22af707a0>
> .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: 0x62e22af707a0>
> 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: 0x62e22bf42680>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x62e22bf42680>
> .Call("R_bm_AddColumn",P)
<pointer: 0x62e22bf42680>
> .Call("R_bm_AddColumn",P)
<pointer: 0x62e22bf42680>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile299ba948a11542" "BufferedMatrixFile299ba976c5551f"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile299ba948a11542" "BufferedMatrixFile299ba976c5551f"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x62e22bcd6490>
> .Call("R_bm_AddColumn",P)
<pointer: 0x62e22bcd6490>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x62e22bcd6490>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x62e22bcd6490>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x62e22bcd6490>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x62e22bcd6490>
> .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: 0x62e22d332110>
> .Call("R_bm_AddColumn",P)
<pointer: 0x62e22d332110>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x62e22d332110>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x62e22d332110>
> 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: 0x62e22d3d55e0>
> .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: 0x62e22d3d55e0>
> rm(P)
>
> proc.time()
user system elapsed
0.241 0.054 0.280
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
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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
0.226 0.062 0.275