Ben Bolstad
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/BufferedMatrix |
| Branch: master |
| Last Commit: d49733d |
| Last Changed Date: 2019-10-29 13:34:45 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:30:37 -0500 (Thu, 16 Jan 2020).
| Package 204/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BufferedMatrix 1.51.0 Ben Bolstad
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: BufferedMatrix |
| Version: 1.51.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BufferedMatrix_1.51.0.tar.gz |
| StartedAt: 2020-01-16 02:21:56 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 02:23:18 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 81.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BufferedMatrix_1.51.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/BufferedMatrix.Rcheck’ * using R Under development (unstable) (2019-12-14 r77572) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BufferedMatrix/DESCRIPTION’ ... OK * this is package ‘BufferedMatrix’ version ‘1.51.0’ * 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 * 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 R 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 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 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 sizes of PDF files under ‘inst/doc’ ... OK * 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 in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/Users/biocbuild/bbs-3.11-bioc/meat/BufferedMatrix.Rcheck/00check.log’ for details.
BufferedMatrix.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BufferedMatrix
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘BufferedMatrix’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c RBufferedMatrix.c -o RBufferedMatrix.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c doubleBufferedMatrix.c -o doubleBufferedMatrix.o
doubleBufferedMatrix.c:1580:7: warning: logical not is only applied to the left hand side of this bitwise operator [-Wlogical-not-parentheses]
if (!(Matrix->readonly) & setting){
^ ~
doubleBufferedMatrix.c:1580:7: note: add parentheses after the '!' to evaluate the bitwise operator first
if (!(Matrix->readonly) & setting){
^
( )
doubleBufferedMatrix.c:1580:7: note: add parentheses around left hand side expression to silence this warning
if (!(Matrix->readonly) & setting){
^
( )
doubleBufferedMatrix.c:3327:12: warning: unused function 'sort_double' [-Wunused-function]
static int sort_double(const double *a1,const double *a2){
^
2 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c doubleBufferedMatrix_C_tests.c -o doubleBufferedMatrix_C_tests.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c init_package.c -o init_package.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o BufferedMatrix.so RBufferedMatrix.o doubleBufferedMatrix.o doubleBufferedMatrix_C_tests.o init_package.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/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) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
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
0.655 0.253 0.887
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
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] "/Users/biocbuild/bbs-3.11-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) limit (Mb) max used (Mb)
Ncells 436192 23.3 939642 50.2 NA 613240 32.8
Vcells 794252 6.1 8388608 64.0 57344 1925579 14.7
>
>
>
>
> ##
> ## 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 Jan 16 02:22:31 2020"
> 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 Jan 16 02:22:32 2020"
>
>
> 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: 0x7fa4aaf00000>
>
>
>
> 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 Jan 16 02:22:41 2020"
> 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 Jan 16 02:22:43 2020"
>
> ColMode(tmp2)
<pointer: 0x7fa4aaf00000>
>
>
>
> ### 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,] 100.22365440 -1.4383998 0.3213328 0.7691372
[2,] -0.00458162 -0.5204305 -0.2289651 -0.1647033
[3,] -0.90515477 0.3016663 -1.0856307 0.8925107
[4,] 0.13940984 -0.7502074 -1.3922005 1.0762080
> ewApply(tmp5,abs)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.11-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 100.22365440 1.4383998 0.3213328 0.7691372
[2,] 0.00458162 0.5204305 0.2289651 0.1647033
[3,] 0.90515477 0.3016663 1.0856307 0.8925107
[4,] 0.13940984 0.7502074 1.3922005 1.0762080
> ewApply(tmp5,sqrt)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.11-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 10.01117647 1.1993331 0.5668622 0.8770047
[2,] 0.06768767 0.7214087 0.4785030 0.4058365
[3,] 0.95139622 0.5492416 1.0419360 0.9447279
[4,] 0.37337627 0.8661451 1.1799154 1.0374045
>
> 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: /Users/biocbuild/bbs-3.11-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 225.33542 38.43173 30.98995 34.53918
[2,] 25.68146 32.73452 30.01399 29.22307
[3,] 35.41912 30.79408 36.50499 35.33979
[4,] 28.87317 34.41166 38.19135 36.45025
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x7fa4aab162f0>
> exp(tmp5)
<pointer: 0x7fa4aab162f0>
> log(tmp5,2)
<pointer: 0x7fa4aab162f0>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 469.0062
> Min(tmp5)
[1] 52.4792
> mean(tmp5)
[1] 71.86726
> Sum(tmp5)
[1] 14373.45
> Var(tmp5)
[1] 867.4237
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 87.13614 70.34676 67.05792 69.28744 69.63975 72.68117 68.63148 72.47461
[9] 72.03395 69.38341
> rowSums(tmp5)
[1] 1742.723 1406.935 1341.158 1385.749 1392.795 1453.623 1372.630 1449.492
[9] 1440.679 1387.668
> rowVars(tmp5)
[1] 8125.17750 91.47771 66.99327 100.87254 39.66845 72.92588
[7] 59.91060 73.45205 77.80647 73.78861
> rowSd(tmp5)
[1] 90.139766 9.564398 8.184942 10.043532 6.298289 8.539665 7.740194
[8] 8.570417 8.820798 8.590030
> rowMax(tmp5)
[1] 469.00615 87.65759 84.82933 84.12617 77.67691 86.23145 79.96218
[8] 84.93529 89.46242 89.48251
> rowMin(tmp5)
[1] 55.81196 53.45259 55.62694 52.58347 59.70446 61.24530 52.47920 53.84640
[9] 56.53221 57.61547
>
> colMeans(tmp5)
[1] 107.93611 71.77963 72.20384 71.21901 67.72173 70.99489 74.51508
[8] 64.55329 67.54257 65.14764 73.29862 71.95185 66.27076 71.85255
[15] 69.58769 74.54868 70.96064 68.53195 66.30584 70.42290
> colSums(tmp5)
[1] 1079.3611 717.7963 722.0384 712.1901 677.2173 709.9489 745.1508
[8] 645.5329 675.4257 651.4764 732.9862 719.5185 662.7076 718.5255
[15] 695.8769 745.4868 709.6064 685.3195 663.0584 704.2290
> colVars(tmp5)
[1] 16140.73709 55.11389 43.20758 70.96216 42.84601 84.00774
[7] 71.22670 75.25517 57.88286 38.23778 129.46009 80.18848
[13] 74.45808 74.12902 67.76703 59.13155 45.42505 100.20249
[19] 92.83191 71.59123
> colSd(tmp5)
[1] 127.046201 7.423873 6.573247 8.423904 6.545686 9.165573
[7] 8.439591 8.674974 7.608079 6.183670 11.378053 8.954802
[13] 8.628910 8.609821 8.232073 7.689704 6.739811 10.010119
[19] 9.634932 8.461160
> colMax(tmp5)
[1] 469.00615 80.66825 80.35865 83.53735 76.71229 83.06171 89.46242
[8] 79.82060 82.51505 74.90713 89.48251 86.23145 83.71774 86.17588
[15] 84.12617 86.04564 80.63816 84.93529 87.65759 84.82933
> colMin(tmp5)
[1] 53.45259 58.85189 62.47020 58.84459 57.61547 55.38458 58.38632 52.47920
[9] 58.77969 57.05505 56.53221 59.52333 56.82221 57.68491 55.78634 63.77392
[17] 60.57484 52.58347 53.84640 56.59483
>
>
> ### 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] 87.13614 70.34676 67.05792 69.28744 69.63975 72.68117 68.63148 NA
[9] 72.03395 69.38341
> rowSums(tmp5)
[1] 1742.723 1406.935 1341.158 1385.749 1392.795 1453.623 1372.630 NA
[9] 1440.679 1387.668
> rowVars(tmp5)
[1] 8125.17750 91.47771 66.99327 100.87254 39.66845 72.92588
[7] 59.91060 70.97794 77.80647 73.78861
> rowSd(tmp5)
[1] 90.139766 9.564398 8.184942 10.043532 6.298289 8.539665 7.740194
[8] 8.424841 8.820798 8.590030
> rowMax(tmp5)
[1] 469.00615 87.65759 84.82933 84.12617 77.67691 86.23145 79.96218
[8] NA 89.46242 89.48251
> rowMin(tmp5)
[1] 55.81196 53.45259 55.62694 52.58347 59.70446 61.24530 52.47920 NA
[9] 56.53221 57.61547
>
> colMeans(tmp5)
[1] 107.93611 71.77963 72.20384 71.21901 67.72173 NA 74.51508
[8] 64.55329 67.54257 65.14764 73.29862 71.95185 66.27076 71.85255
[15] 69.58769 74.54868 70.96064 68.53195 66.30584 70.42290
> colSums(tmp5)
[1] 1079.3611 717.7963 722.0384 712.1901 677.2173 NA 745.1508
[8] 645.5329 675.4257 651.4764 732.9862 719.5185 662.7076 718.5255
[15] 695.8769 745.4868 709.6064 685.3195 663.0584 704.2290
> colVars(tmp5)
[1] 16140.73709 55.11389 43.20758 70.96216 42.84601 NA
[7] 71.22670 75.25517 57.88286 38.23778 129.46009 80.18848
[13] 74.45808 74.12902 67.76703 59.13155 45.42505 100.20249
[19] 92.83191 71.59123
> colSd(tmp5)
[1] 127.046201 7.423873 6.573247 8.423904 6.545686 NA
[7] 8.439591 8.674974 7.608079 6.183670 11.378053 8.954802
[13] 8.628910 8.609821 8.232073 7.689704 6.739811 10.010119
[19] 9.634932 8.461160
> colMax(tmp5)
[1] 469.00615 80.66825 80.35865 83.53735 76.71229 NA 89.46242
[8] 79.82060 82.51505 74.90713 89.48251 86.23145 83.71774 86.17588
[15] 84.12617 86.04564 80.63816 84.93529 87.65759 84.82933
> colMin(tmp5)
[1] 53.45259 58.85189 62.47020 58.84459 57.61547 NA 58.38632 52.47920
[9] 58.77969 57.05505 56.53221 59.52333 56.82221 57.68491 55.78634 63.77392
[17] 60.57484 52.58347 53.84640 56.59483
>
> Max(tmp5,na.rm=TRUE)
[1] 469.0062
> Min(tmp5,na.rm=TRUE)
[1] 52.4792
> mean(tmp5,na.rm=TRUE)
[1] 71.81101
> Sum(tmp5,na.rm=TRUE)
[1] 14290.39
> Var(tmp5,na.rm=TRUE)
[1] 871.1686
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 87.13614 70.34676 67.05792 69.28744 69.63975 72.68117 68.63148 71.91740
[9] 72.03395 69.38341
> rowSums(tmp5,na.rm=TRUE)
[1] 1742.723 1406.935 1341.158 1385.749 1392.795 1453.623 1372.630 1366.431
[9] 1440.679 1387.668
> rowVars(tmp5,na.rm=TRUE)
[1] 8125.17750 91.47771 66.99327 100.87254 39.66845 72.92588
[7] 59.91060 70.97794 77.80647 73.78861
> rowSd(tmp5,na.rm=TRUE)
[1] 90.139766 9.564398 8.184942 10.043532 6.298289 8.539665 7.740194
[8] 8.424841 8.820798 8.590030
> rowMax(tmp5,na.rm=TRUE)
[1] 469.00615 87.65759 84.82933 84.12617 77.67691 86.23145 79.96218
[8] 84.93529 89.46242 89.48251
> rowMin(tmp5,na.rm=TRUE)
[1] 55.81196 53.45259 55.62694 52.58347 59.70446 61.24530 52.47920 53.84640
[9] 56.53221 57.61547
>
> colMeans(tmp5,na.rm=TRUE)
[1] 107.93611 71.77963 72.20384 71.21901 67.72173 69.65414 74.51508
[8] 64.55329 67.54257 65.14764 73.29862 71.95185 66.27076 71.85255
[15] 69.58769 74.54868 70.96064 68.53195 66.30584 70.42290
> colSums(tmp5,na.rm=TRUE)
[1] 1079.3611 717.7963 722.0384 712.1901 677.2173 626.8872 745.1508
[8] 645.5329 675.4257 651.4764 732.9862 719.5185 662.7076 718.5255
[15] 695.8769 745.4868 709.6064 685.3195 663.0584 704.2290
> colVars(tmp5,na.rm=TRUE)
[1] 16140.73709 55.11389 43.20758 70.96216 42.84601 74.28537
[7] 71.22670 75.25517 57.88286 38.23778 129.46009 80.18848
[13] 74.45808 74.12902 67.76703 59.13155 45.42505 100.20249
[19] 92.83191 71.59123
> colSd(tmp5,na.rm=TRUE)
[1] 127.046201 7.423873 6.573247 8.423904 6.545686 8.618896
[7] 8.439591 8.674974 7.608079 6.183670 11.378053 8.954802
[13] 8.628910 8.609821 8.232073 7.689704 6.739811 10.010119
[19] 9.634932 8.461160
> colMax(tmp5,na.rm=TRUE)
[1] 469.00615 80.66825 80.35865 83.53735 76.71229 78.86540 89.46242
[8] 79.82060 82.51505 74.90713 89.48251 86.23145 83.71774 86.17588
[15] 84.12617 86.04564 80.63816 84.93529 87.65759 84.82933
> colMin(tmp5,na.rm=TRUE)
[1] 53.45259 58.85189 62.47020 58.84459 57.61547 55.38458 58.38632 52.47920
[9] 58.77969 57.05505 56.53221 59.52333 56.82221 57.68491 55.78634 63.77392
[17] 60.57484 52.58347 53.84640 56.59483
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 87.13614 70.34676 67.05792 69.28744 69.63975 72.68117 68.63148 NaN
[9] 72.03395 69.38341
> rowSums(tmp5,na.rm=TRUE)
[1] 1742.723 1406.935 1341.158 1385.749 1392.795 1453.623 1372.630 0.000
[9] 1440.679 1387.668
> rowVars(tmp5,na.rm=TRUE)
[1] 8125.17750 91.47771 66.99327 100.87254 39.66845 72.92588
[7] 59.91060 NA 77.80647 73.78861
> rowSd(tmp5,na.rm=TRUE)
[1] 90.139766 9.564398 8.184942 10.043532 6.298289 8.539665 7.740194
[8] NA 8.820798 8.590030
> rowMax(tmp5,na.rm=TRUE)
[1] 469.00615 87.65759 84.82933 84.12617 77.67691 86.23145 79.96218
[8] NA 89.46242 89.48251
> rowMin(tmp5,na.rm=TRUE)
[1] 55.81196 53.45259 55.62694 52.58347 59.70446 61.24530 52.47920 NA
[9] 56.53221 57.61547
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 111.56986 71.27936 71.29775 71.21372 66.87463 NaN 74.70820
[8] 64.61889 67.68810 65.99891 72.03349 71.12958 64.85841 71.95255
[15] 69.09711 75.74588 71.21515 66.70935 67.69022 70.66031
> colSums(tmp5,na.rm=TRUE)
[1] 1004.1287 641.5143 641.6798 640.9235 601.8717 0.0000 672.3738
[8] 581.5700 609.1929 593.9902 648.3014 640.1662 583.7256 647.5729
[15] 621.8740 681.7129 640.9363 600.3842 609.2120 635.9428
> colVars(tmp5,na.rm=TRUE)
[1] 18009.78264 59.18757 39.37229 79.83212 40.12901 NA
[7] 79.71045 84.61365 64.87995 34.86498 127.63641 82.60563
[13] 61.32453 83.28267 73.53038 50.39862 50.37447 75.35703
[19] 82.87511 79.90607
> colSd(tmp5,na.rm=TRUE)
[1] 134.200531 7.693346 6.274734 8.934882 6.334746 NA
[7] 8.928071 9.198568 8.054809 5.904657 11.297628 9.088764
[13] 7.830998 9.125934 8.574986 7.099198 7.097497 8.680843
[19] 9.103577 8.939019
> colMax(tmp5,na.rm=TRUE)
[1] 469.00615 80.66825 79.49030 83.53735 76.71229 -Inf 89.46242
[8] 79.82060 82.51505 74.90713 89.48251 86.23145 83.71774 86.17588
[15] 84.12617 86.04564 80.63816 82.08136 87.65759 84.82933
> colMin(tmp5,na.rm=TRUE)
[1] 53.45259 58.85189 62.47020 58.84459 57.61547 Inf 58.38632 52.47920
[9] 58.77969 57.05505 56.53221 59.52333 56.82221 57.68491 55.78634 64.51218
[17] 60.57484 52.58347 60.55659 56.59483
>
>
>
>
> 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] 209.1274 217.5243 149.2622 307.6934 163.3477 190.3177 174.1755 311.5681
[9] 184.7012 268.2842
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 209.1274 217.5243 149.2622 307.6934 163.3477 190.3177 174.1755 311.5681
[9] 184.7012 268.2842
>
>
>
> 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 -8.526513e-14 5.684342e-14 0.000000e+00 -2.842171e-14
[6] 0.000000e+00 1.989520e-13 6.394885e-14 -1.136868e-13 1.136868e-13
[11] -5.684342e-14 -5.684342e-14 2.842171e-14 0.000000e+00 1.278977e-13
[16] -1.989520e-13 -8.526513e-14 -5.684342e-14 -1.421085e-13 -5.684342e-14
>
>
>
>
>
>
>
>
>
>
> ## making sure these things agree
> ##
> ## first when there is no NA
>
>
>
> agree.checks <- function(buff.matrix,r.matrix,err.tol=1e-10){
+
+ if (Max(buff.matrix,na.rm=TRUE) != max(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Max")
+ }
+
+
+ if (Min(buff.matrix,na.rm=TRUE) != min(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Min")
+ }
+
+
+ if (abs(Sum(buff.matrix,na.rm=TRUE)- sum(r.matrix,na.rm=TRUE)) > err.tol){
+
+ cat(Sum(buff.matrix,na.rm=TRUE),"\n")
+ cat(sum(r.matrix,na.rm=TRUE),"\n")
+ cat(Sum(buff.matrix,na.rm=TRUE) - sum(r.matrix,na.rm=TRUE),"\n")
+
+ stop("No agreement in Sum")
+ }
+
+ if (abs(mean(buff.matrix,na.rm=TRUE) - mean(r.matrix,na.rm=TRUE)) > err.tol){
+ stop("No agreement in mean")
+ }
+
+
+ if(abs(Var(buff.matrix,na.rm=TRUE) - var(as.vector(r.matrix),na.rm=TRUE)) > err.tol){
+ stop("No agreement in Var")
+ }
+
+
+
+ if(any(abs(rowMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,mean,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowMeans")
+ }
+
+
+ if(any(abs(colMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,mean,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colMeans")
+ }
+
+
+ if(any(abs(rowSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in rowSums")
+ }
+
+
+ if(any(abs(colSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colSums")
+ }
+
+ ### this is to get around the fact that R doesn't like to compute NA on an entire vector of NA when
+ ### computing variance
+ my.Var <- function(x,na.rm=FALSE){
+ if (all(is.na(x))){
+ return(NA)
+ } else {
+ var(x,na.rm=na.rm)
+ }
+
+ }
+
+ if(any(abs(rowVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(colVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(rowMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+ if(any(abs(colMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+
+ if(any(abs(rowMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+
+ if(any(abs(colMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+ if(any(abs(colMedians(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,median,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMedian")
+ }
+
+ if(any(abs(colRanges(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,range,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colRanges")
+ }
+
+
+
+ }
>
>
>
>
>
>
>
>
>
> for (rep in 1:20){
+ copymatrix <- matrix(rnorm(200,150,15),10,20)
+
+ tmp5[1:10,1:20] <- copymatrix
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ## now lets assign some NA values and check agreement
+
+ which.row <- sample(1:10,1,replace=TRUE)
+ which.col <- sample(1:20,1,replace=TRUE)
+
+ cat(which.row," ",which.col,"\n")
+
+ tmp5[which.row,which.col] <- NA
+ copymatrix[which.row,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ## make an entire row NA
+ tmp5[which.row,] <- NA
+ copymatrix[which.row,] <- NA
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ### also make an entire col NA
+ tmp5[,which.col] <- NA
+ copymatrix[,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ### now make 1 element non NA with NA in the rest of row and column
+
+ tmp5[which.row,which.col] <- rnorm(1,150,15)
+ copymatrix[which.row,which.col] <- tmp5[which.row,which.col]
+
+ agree.checks(tmp5,copymatrix)
+ }
4 2
2 13
4 1
7 13
7 1
1 12
9 7
3 20
6 17
2 2
6 5
4 8
7 2
5 2
2 11
4 9
7 6
6 19
6 13
10 18
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] 2.021676
> Min(tmp)
[1] -2.194107
> mean(tmp)
[1] -0.1116496
> Sum(tmp)
[1] -11.16496
> Var(tmp)
[1] 0.7983616
>
> rowMeans(tmp)
[1] -0.1116496
> rowSums(tmp)
[1] -11.16496
> rowVars(tmp)
[1] 0.7983616
> rowSd(tmp)
[1] 0.8935108
> rowMax(tmp)
[1] 2.021676
> rowMin(tmp)
[1] -2.194107
>
> colMeans(tmp)
[1] -0.55453875 -0.82175565 -0.67508276 1.37678469 -1.30559095 -0.01849659
[7] 0.51610652 0.27062140 -0.44757098 -0.88197208 0.29138475 1.82763445
[13] 0.22583715 -0.23984503 1.06178172 -1.10849154 0.92805381 1.79779249
[19] 0.70124979 0.46727958 -1.18605197 -0.74993128 0.50471143 -2.05733335
[25] -0.27737599 0.60182852 1.44959770 -0.62807126 0.68684821 0.02475166
[31] 0.44041621 -0.88263521 -0.77340752 -0.50054568 0.70419077 0.07128037
[37] -0.15734885 0.86581062 2.02167635 0.51219526 0.05835508 -1.26712922
[43] -0.19105790 0.22867336 -0.67885555 -0.17282169 0.21108856 0.49652454
[49] -1.81687306 0.39512251 0.55141154 -2.19410705 0.27554164 -1.76126618
[55] 0.83669333 0.37873492 -1.26416700 -0.67771525 -1.37092526 -0.11289677
[61] -0.97265251 -0.46459574 -1.23654431 0.75497972 -0.32847769 -0.36774563
[67] 0.28828231 1.08164025 -0.39454123 -1.02993713 -1.02803666 -1.28607654
[73] 0.66004704 -0.12591463 -1.01346301 0.22176613 1.05000588 0.83182927
[79] 0.27096866 0.62449293 0.34383230 -0.72389793 -1.18721372 -0.42117231
[85] -0.44882241 -0.99906453 0.27168164 0.13697768 0.74650151 0.55987324
[91] -2.00750985 -0.05948283 -1.23508678 1.21837233 -0.98688416 -1.03446527
[97] 0.64828706 -0.35863779 0.58108546 0.24852486
> colSums(tmp)
[1] -0.55453875 -0.82175565 -0.67508276 1.37678469 -1.30559095 -0.01849659
[7] 0.51610652 0.27062140 -0.44757098 -0.88197208 0.29138475 1.82763445
[13] 0.22583715 -0.23984503 1.06178172 -1.10849154 0.92805381 1.79779249
[19] 0.70124979 0.46727958 -1.18605197 -0.74993128 0.50471143 -2.05733335
[25] -0.27737599 0.60182852 1.44959770 -0.62807126 0.68684821 0.02475166
[31] 0.44041621 -0.88263521 -0.77340752 -0.50054568 0.70419077 0.07128037
[37] -0.15734885 0.86581062 2.02167635 0.51219526 0.05835508 -1.26712922
[43] -0.19105790 0.22867336 -0.67885555 -0.17282169 0.21108856 0.49652454
[49] -1.81687306 0.39512251 0.55141154 -2.19410705 0.27554164 -1.76126618
[55] 0.83669333 0.37873492 -1.26416700 -0.67771525 -1.37092526 -0.11289677
[61] -0.97265251 -0.46459574 -1.23654431 0.75497972 -0.32847769 -0.36774563
[67] 0.28828231 1.08164025 -0.39454123 -1.02993713 -1.02803666 -1.28607654
[73] 0.66004704 -0.12591463 -1.01346301 0.22176613 1.05000588 0.83182927
[79] 0.27096866 0.62449293 0.34383230 -0.72389793 -1.18721372 -0.42117231
[85] -0.44882241 -0.99906453 0.27168164 0.13697768 0.74650151 0.55987324
[91] -2.00750985 -0.05948283 -1.23508678 1.21837233 -0.98688416 -1.03446527
[97] 0.64828706 -0.35863779 0.58108546 0.24852486
> colVars(tmp)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> colSd(tmp)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> colMax(tmp)
[1] -0.55453875 -0.82175565 -0.67508276 1.37678469 -1.30559095 -0.01849659
[7] 0.51610652 0.27062140 -0.44757098 -0.88197208 0.29138475 1.82763445
[13] 0.22583715 -0.23984503 1.06178172 -1.10849154 0.92805381 1.79779249
[19] 0.70124979 0.46727958 -1.18605197 -0.74993128 0.50471143 -2.05733335
[25] -0.27737599 0.60182852 1.44959770 -0.62807126 0.68684821 0.02475166
[31] 0.44041621 -0.88263521 -0.77340752 -0.50054568 0.70419077 0.07128037
[37] -0.15734885 0.86581062 2.02167635 0.51219526 0.05835508 -1.26712922
[43] -0.19105790 0.22867336 -0.67885555 -0.17282169 0.21108856 0.49652454
[49] -1.81687306 0.39512251 0.55141154 -2.19410705 0.27554164 -1.76126618
[55] 0.83669333 0.37873492 -1.26416700 -0.67771525 -1.37092526 -0.11289677
[61] -0.97265251 -0.46459574 -1.23654431 0.75497972 -0.32847769 -0.36774563
[67] 0.28828231 1.08164025 -0.39454123 -1.02993713 -1.02803666 -1.28607654
[73] 0.66004704 -0.12591463 -1.01346301 0.22176613 1.05000588 0.83182927
[79] 0.27096866 0.62449293 0.34383230 -0.72389793 -1.18721372 -0.42117231
[85] -0.44882241 -0.99906453 0.27168164 0.13697768 0.74650151 0.55987324
[91] -2.00750985 -0.05948283 -1.23508678 1.21837233 -0.98688416 -1.03446527
[97] 0.64828706 -0.35863779 0.58108546 0.24852486
> colMin(tmp)
[1] -0.55453875 -0.82175565 -0.67508276 1.37678469 -1.30559095 -0.01849659
[7] 0.51610652 0.27062140 -0.44757098 -0.88197208 0.29138475 1.82763445
[13] 0.22583715 -0.23984503 1.06178172 -1.10849154 0.92805381 1.79779249
[19] 0.70124979 0.46727958 -1.18605197 -0.74993128 0.50471143 -2.05733335
[25] -0.27737599 0.60182852 1.44959770 -0.62807126 0.68684821 0.02475166
[31] 0.44041621 -0.88263521 -0.77340752 -0.50054568 0.70419077 0.07128037
[37] -0.15734885 0.86581062 2.02167635 0.51219526 0.05835508 -1.26712922
[43] -0.19105790 0.22867336 -0.67885555 -0.17282169 0.21108856 0.49652454
[49] -1.81687306 0.39512251 0.55141154 -2.19410705 0.27554164 -1.76126618
[55] 0.83669333 0.37873492 -1.26416700 -0.67771525 -1.37092526 -0.11289677
[61] -0.97265251 -0.46459574 -1.23654431 0.75497972 -0.32847769 -0.36774563
[67] 0.28828231 1.08164025 -0.39454123 -1.02993713 -1.02803666 -1.28607654
[73] 0.66004704 -0.12591463 -1.01346301 0.22176613 1.05000588 0.83182927
[79] 0.27096866 0.62449293 0.34383230 -0.72389793 -1.18721372 -0.42117231
[85] -0.44882241 -0.99906453 0.27168164 0.13697768 0.74650151 0.55987324
[91] -2.00750985 -0.05948283 -1.23508678 1.21837233 -0.98688416 -1.03446527
[97] 0.64828706 -0.35863779 0.58108546 0.24852486
> colMedians(tmp)
[1] -0.55453875 -0.82175565 -0.67508276 1.37678469 -1.30559095 -0.01849659
[7] 0.51610652 0.27062140 -0.44757098 -0.88197208 0.29138475 1.82763445
[13] 0.22583715 -0.23984503 1.06178172 -1.10849154 0.92805381 1.79779249
[19] 0.70124979 0.46727958 -1.18605197 -0.74993128 0.50471143 -2.05733335
[25] -0.27737599 0.60182852 1.44959770 -0.62807126 0.68684821 0.02475166
[31] 0.44041621 -0.88263521 -0.77340752 -0.50054568 0.70419077 0.07128037
[37] -0.15734885 0.86581062 2.02167635 0.51219526 0.05835508 -1.26712922
[43] -0.19105790 0.22867336 -0.67885555 -0.17282169 0.21108856 0.49652454
[49] -1.81687306 0.39512251 0.55141154 -2.19410705 0.27554164 -1.76126618
[55] 0.83669333 0.37873492 -1.26416700 -0.67771525 -1.37092526 -0.11289677
[61] -0.97265251 -0.46459574 -1.23654431 0.75497972 -0.32847769 -0.36774563
[67] 0.28828231 1.08164025 -0.39454123 -1.02993713 -1.02803666 -1.28607654
[73] 0.66004704 -0.12591463 -1.01346301 0.22176613 1.05000588 0.83182927
[79] 0.27096866 0.62449293 0.34383230 -0.72389793 -1.18721372 -0.42117231
[85] -0.44882241 -0.99906453 0.27168164 0.13697768 0.74650151 0.55987324
[91] -2.00750985 -0.05948283 -1.23508678 1.21837233 -0.98688416 -1.03446527
[97] 0.64828706 -0.35863779 0.58108546 0.24852486
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] -0.5545387 -0.8217557 -0.6750828 1.376785 -1.305591 -0.01849659 0.5161065
[2,] -0.5545387 -0.8217557 -0.6750828 1.376785 -1.305591 -0.01849659 0.5161065
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] 0.2706214 -0.447571 -0.8819721 0.2913847 1.827634 0.2258372 -0.239845
[2,] 0.2706214 -0.447571 -0.8819721 0.2913847 1.827634 0.2258372 -0.239845
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] 1.061782 -1.108492 0.9280538 1.797792 0.7012498 0.4672796 -1.186052
[2,] 1.061782 -1.108492 0.9280538 1.797792 0.7012498 0.4672796 -1.186052
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] -0.7499313 0.5047114 -2.057333 -0.277376 0.6018285 1.449598 -0.6280713
[2,] -0.7499313 0.5047114 -2.057333 -0.277376 0.6018285 1.449598 -0.6280713
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] 0.6868482 0.02475166 0.4404162 -0.8826352 -0.7734075 -0.5005457 0.7041908
[2,] 0.6868482 0.02475166 0.4404162 -0.8826352 -0.7734075 -0.5005457 0.7041908
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] 0.07128037 -0.1573489 0.8658106 2.021676 0.5121953 0.05835508 -1.267129
[2,] 0.07128037 -0.1573489 0.8658106 2.021676 0.5121953 0.05835508 -1.267129
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] -0.1910579 0.2286734 -0.6788555 -0.1728217 0.2110886 0.4965245 -1.816873
[2,] -0.1910579 0.2286734 -0.6788555 -0.1728217 0.2110886 0.4965245 -1.816873
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] 0.3951225 0.5514115 -2.194107 0.2755416 -1.761266 0.8366933 0.3787349
[2,] 0.3951225 0.5514115 -2.194107 0.2755416 -1.761266 0.8366933 0.3787349
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] -1.264167 -0.6777152 -1.370925 -0.1128968 -0.9726525 -0.4645957 -1.236544
[2,] -1.264167 -0.6777152 -1.370925 -0.1128968 -0.9726525 -0.4645957 -1.236544
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] 0.7549797 -0.3284777 -0.3677456 0.2882823 1.08164 -0.3945412 -1.029937
[2,] 0.7549797 -0.3284777 -0.3677456 0.2882823 1.08164 -0.3945412 -1.029937
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] -1.028037 -1.286077 0.660047 -0.1259146 -1.013463 0.2217661 1.050006
[2,] -1.028037 -1.286077 0.660047 -0.1259146 -1.013463 0.2217661 1.050006
[,78] [,79] [,80] [,81] [,82] [,83] [,84]
[1,] 0.8318293 0.2709687 0.6244929 0.3438323 -0.7238979 -1.187214 -0.4211723
[2,] 0.8318293 0.2709687 0.6244929 0.3438323 -0.7238979 -1.187214 -0.4211723
[,85] [,86] [,87] [,88] [,89] [,90] [,91]
[1,] -0.4488224 -0.9990645 0.2716816 0.1369777 0.7465015 0.5598732 -2.00751
[2,] -0.4488224 -0.9990645 0.2716816 0.1369777 0.7465015 0.5598732 -2.00751
[,92] [,93] [,94] [,95] [,96] [,97] [,98]
[1,] -0.05948283 -1.235087 1.218372 -0.9868842 -1.034465 0.6482871 -0.3586378
[2,] -0.05948283 -1.235087 1.218372 -0.9868842 -1.034465 0.6482871 -0.3586378
[,99] [,100]
[1,] 0.5810855 0.2485249
[2,] 0.5810855 0.2485249
>
>
> Max(tmp2)
[1] 2.285368
> Min(tmp2)
[1] -2.596974
> mean(tmp2)
[1] 0.1105926
> Sum(tmp2)
[1] 11.05926
> Var(tmp2)
[1] 0.9181488
>
> rowMeans(tmp2)
[1] 1.28217196 0.60783898 0.20324717 -0.26889064 1.97616952 1.42092053
[7] 1.62164547 -1.03771172 0.95854696 0.58351574 0.46097829 0.37169285
[13] 0.52165827 0.09841024 -0.64519302 -2.01285914 0.90946679 0.76655539
[19] -0.06169205 2.28536777 -2.06017546 -1.07423724 0.41228201 -0.87046661
[25] 1.11610062 1.05607254 -0.28878889 -0.01276645 -0.40204467 0.66086555
[31] -0.71412411 -0.76680548 -0.55486712 -0.26953555 -1.32605767 0.48281425
[37] 1.58188205 -1.18194286 0.56122341 0.42129628 0.34176806 1.42472826
[43] 0.38004164 0.48477412 0.97793298 -0.03168923 -0.14150573 0.92521529
[49] 0.37130123 1.38976937 1.28757370 -0.58508739 -2.01680403 0.31501759
[55] 0.14632906 0.44761473 0.37939493 -0.36762892 -0.63466174 0.88728112
[61] -1.71664733 0.22751267 -0.88681680 0.26198418 1.49194265 -0.90072658
[67] 0.33065862 1.09086319 0.23134433 -0.53799914 -0.35218636 -0.75422865
[73] 1.25732265 -0.43038547 0.53984478 0.30705425 -2.59697412 -1.67822614
[79] -0.32504792 -0.30165891 -0.91420159 -0.51498611 1.19758675 0.54849016
[85] 1.09656572 -0.06399832 0.68935063 -1.30273656 0.33635296 0.39077080
[91] -0.04936789 0.39362647 -0.08192799 1.49492486 -0.28490841 -1.11896082
[97] -0.05578890 1.76716157 -1.04560677 0.52535623
> rowSums(tmp2)
[1] 1.28217196 0.60783898 0.20324717 -0.26889064 1.97616952 1.42092053
[7] 1.62164547 -1.03771172 0.95854696 0.58351574 0.46097829 0.37169285
[13] 0.52165827 0.09841024 -0.64519302 -2.01285914 0.90946679 0.76655539
[19] -0.06169205 2.28536777 -2.06017546 -1.07423724 0.41228201 -0.87046661
[25] 1.11610062 1.05607254 -0.28878889 -0.01276645 -0.40204467 0.66086555
[31] -0.71412411 -0.76680548 -0.55486712 -0.26953555 -1.32605767 0.48281425
[37] 1.58188205 -1.18194286 0.56122341 0.42129628 0.34176806 1.42472826
[43] 0.38004164 0.48477412 0.97793298 -0.03168923 -0.14150573 0.92521529
[49] 0.37130123 1.38976937 1.28757370 -0.58508739 -2.01680403 0.31501759
[55] 0.14632906 0.44761473 0.37939493 -0.36762892 -0.63466174 0.88728112
[61] -1.71664733 0.22751267 -0.88681680 0.26198418 1.49194265 -0.90072658
[67] 0.33065862 1.09086319 0.23134433 -0.53799914 -0.35218636 -0.75422865
[73] 1.25732265 -0.43038547 0.53984478 0.30705425 -2.59697412 -1.67822614
[79] -0.32504792 -0.30165891 -0.91420159 -0.51498611 1.19758675 0.54849016
[85] 1.09656572 -0.06399832 0.68935063 -1.30273656 0.33635296 0.39077080
[91] -0.04936789 0.39362647 -0.08192799 1.49492486 -0.28490841 -1.11896082
[97] -0.05578890 1.76716157 -1.04560677 0.52535623
> 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] 1.28217196 0.60783898 0.20324717 -0.26889064 1.97616952 1.42092053
[7] 1.62164547 -1.03771172 0.95854696 0.58351574 0.46097829 0.37169285
[13] 0.52165827 0.09841024 -0.64519302 -2.01285914 0.90946679 0.76655539
[19] -0.06169205 2.28536777 -2.06017546 -1.07423724 0.41228201 -0.87046661
[25] 1.11610062 1.05607254 -0.28878889 -0.01276645 -0.40204467 0.66086555
[31] -0.71412411 -0.76680548 -0.55486712 -0.26953555 -1.32605767 0.48281425
[37] 1.58188205 -1.18194286 0.56122341 0.42129628 0.34176806 1.42472826
[43] 0.38004164 0.48477412 0.97793298 -0.03168923 -0.14150573 0.92521529
[49] 0.37130123 1.38976937 1.28757370 -0.58508739 -2.01680403 0.31501759
[55] 0.14632906 0.44761473 0.37939493 -0.36762892 -0.63466174 0.88728112
[61] -1.71664733 0.22751267 -0.88681680 0.26198418 1.49194265 -0.90072658
[67] 0.33065862 1.09086319 0.23134433 -0.53799914 -0.35218636 -0.75422865
[73] 1.25732265 -0.43038547 0.53984478 0.30705425 -2.59697412 -1.67822614
[79] -0.32504792 -0.30165891 -0.91420159 -0.51498611 1.19758675 0.54849016
[85] 1.09656572 -0.06399832 0.68935063 -1.30273656 0.33635296 0.39077080
[91] -0.04936789 0.39362647 -0.08192799 1.49492486 -0.28490841 -1.11896082
[97] -0.05578890 1.76716157 -1.04560677 0.52535623
> rowMin(tmp2)
[1] 1.28217196 0.60783898 0.20324717 -0.26889064 1.97616952 1.42092053
[7] 1.62164547 -1.03771172 0.95854696 0.58351574 0.46097829 0.37169285
[13] 0.52165827 0.09841024 -0.64519302 -2.01285914 0.90946679 0.76655539
[19] -0.06169205 2.28536777 -2.06017546 -1.07423724 0.41228201 -0.87046661
[25] 1.11610062 1.05607254 -0.28878889 -0.01276645 -0.40204467 0.66086555
[31] -0.71412411 -0.76680548 -0.55486712 -0.26953555 -1.32605767 0.48281425
[37] 1.58188205 -1.18194286 0.56122341 0.42129628 0.34176806 1.42472826
[43] 0.38004164 0.48477412 0.97793298 -0.03168923 -0.14150573 0.92521529
[49] 0.37130123 1.38976937 1.28757370 -0.58508739 -2.01680403 0.31501759
[55] 0.14632906 0.44761473 0.37939493 -0.36762892 -0.63466174 0.88728112
[61] -1.71664733 0.22751267 -0.88681680 0.26198418 1.49194265 -0.90072658
[67] 0.33065862 1.09086319 0.23134433 -0.53799914 -0.35218636 -0.75422865
[73] 1.25732265 -0.43038547 0.53984478 0.30705425 -2.59697412 -1.67822614
[79] -0.32504792 -0.30165891 -0.91420159 -0.51498611 1.19758675 0.54849016
[85] 1.09656572 -0.06399832 0.68935063 -1.30273656 0.33635296 0.39077080
[91] -0.04936789 0.39362647 -0.08192799 1.49492486 -0.28490841 -1.11896082
[97] -0.05578890 1.76716157 -1.04560677 0.52535623
>
> colMeans(tmp2)
[1] 0.1105926
> colSums(tmp2)
[1] 11.05926
> colVars(tmp2)
[1] 0.9181488
> colSd(tmp2)
[1] 0.9582008
> colMax(tmp2)
[1] 2.285368
> colMin(tmp2)
[1] -2.596974
> colMedians(tmp2)
[1] 0.2845192
> colRanges(tmp2)
[,1]
[1,] -2.596974
[2,] 2.285368
>
> dataset1 <- matrix(dataset1,1,100)
>
> agree.checks(tmp,dataset1)
>
> dataset2 <- matrix(dataset2,100,1)
> agree.checks(tmp2,dataset2)
>
>
> tmp <- createBufferedMatrix(10,10)
>
> tmp[1:10,1:10] <- rnorm(100)
> colApply(tmp,sum)
[1] 1.0903097 4.5426447 -5.4207966 2.7399220 -0.5656708 0.1161714
[7] -5.9373121 -2.9349615 -4.9914760 -3.2667143
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.7525978
[2,] -0.5850257
[3,] 0.2835297
[4,] 0.7893470
[5,] 1.2734040
>
> rowApply(tmp,sum)
[1] -4.3413944 -0.9831134 -1.8195924 -2.2295488 3.3059169 -2.1530456
[7] 1.7676084 -0.4010919 -2.2256947 -5.5479276
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 10 10 2 5 6 6 2 9 8
[2,] 10 8 5 5 9 8 8 9 6 7
[3,] 6 7 3 3 2 4 2 5 5 2
[4,] 8 6 2 9 10 9 10 8 7 3
[5,] 3 4 7 10 4 7 3 7 3 5
[6,] 4 3 4 1 6 10 7 4 10 4
[7,] 9 1 1 4 3 3 4 3 8 1
[8,] 7 2 9 6 7 5 1 10 1 9
[9,] 2 9 8 7 1 2 5 1 2 10
[10,] 5 5 6 8 8 1 9 6 4 6
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] 1.4458686 -1.2858264 0.1096623 -1.1775532 2.9200642 0.4384519
[7] 4.1705072 -1.0979166 3.8054063 -2.1375643 -0.4256915 -1.7857009
[13] 3.1416616 -2.4749171 -2.4584470 1.7083624 -1.4437114 -3.7213225
[19] 2.0614414 -1.9490603
> colApply(tmp,quantile)[,1]
[,1]
[1,] -2.04460124
[2,] -0.04574828
[3,] 0.64131012
[4,] 0.88780810
[5,] 2.00709991
>
> rowApply(tmp,sum)
[1] 3.2547238 -3.4839587 1.9643251 -2.2810273 0.3896516
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 17 2 19 11 14
[2,] 8 10 5 3 10
[3,] 5 11 11 4 19
[4,] 15 4 12 16 3
[5,] 14 17 18 13 7
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 0.88780810 0.1583679 -0.26831370 0.70147377 0.6379231 0.1577180
[2,] -2.04460124 -0.1049048 0.05483266 -1.20077585 0.9730032 0.3034025
[3,] 2.00709991 -0.5142751 -0.07242954 0.07741277 1.6674036 0.6666329
[4,] -0.04574828 -0.9479053 -0.92411694 0.40738617 0.1273363 -1.1214710
[5,] 0.64131012 0.1228909 1.31968985 -1.16305010 -0.4856019 0.4321695
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] 1.3033443 -1.1676249 0.2153472 0.3061380 -2.1251871 0.3039881
[2,] 1.2214393 0.2396563 1.3336697 -0.2889242 0.7832830 -0.9907388
[3,] 0.4938759 -1.1848197 2.3012770 0.6599505 -0.9826937 -0.2161993
[4,] 0.4683611 -0.1087277 0.6853808 -0.6229947 1.3469118 0.2025515
[5,] 0.6834866 1.1235994 -0.7302684 -2.1917340 0.5519944 -1.0853025
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] 0.7482696 -0.2011682 0.3531347 0.8878165 -0.71915665 -1.4307247
[2,] 0.5376634 -0.3964482 -0.9069505 1.0961387 0.60566556 -1.5410121
[3,] -0.3593582 -0.3236405 -0.8559661 0.7137225 -1.54824862 0.4055385
[4,] 0.3074000 -0.1718772 -0.6585410 -0.5467783 -0.03744075 -2.1525218
[5,] 1.9076868 -1.3817830 -0.3901240 -0.4425370 0.25546909 0.9973976
[,19] [,20]
[1,] 1.9991121 0.5064578
[2,] -0.1805441 -2.9778130
[3,] -0.4810131 -0.4899447
[4,] -0.2861403 1.7979085
[5,] 1.0100269 -0.7856689
>
>
> is.BufferedMatrix(tmp)
[1] TRUE
>
> as.BufferedMatrix(as.matrix(tmp))
BufferedMatrix object
Matrix size: 5 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.11-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: /Users/biocbuild/bbs-3.11-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 650 bytes.
Disk usage : 200 bytes.
> subBufferedMatrix(tmp,,5:8)
BufferedMatrix object
Matrix size: 5 4
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.11-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 563 bytes.
Disk usage : 160 bytes.
> subBufferedMatrix(tmp,1:3,)
BufferedMatrix object
Matrix size: 3 20
Buffer size: 1 1
Directory: /Users/biocbuild/bbs-3.11-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 1.026654 0.06477164 0.8964987 -0.6105409 0.4035107 0.880951 0.2854664
col8 col9 col10 col11 col12 col13 col14
row1 0.07900265 0.7988099 0.6073476 -0.2521945 0.9582453 -0.826692 -0.3629321
col15 col16 col17 col18 col19 col20
row1 -0.9731777 -0.4889981 0.600925 0.4533682 -0.1221586 -0.3863065
> tmp[,"col10"]
col10
row1 0.6073476
row2 -1.1055748
row3 1.7820926
row4 0.9689878
row5 0.5570443
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7
row1 1.0266541 0.06477164 0.8964987 -0.6105409 0.4035107 0.8809510 0.2854664
row5 -0.6415162 -1.21316036 0.6322510 1.8368914 0.5611681 -0.5911259 0.9258033
col8 col9 col10 col11 col12 col13
row1 0.07900265 0.7988099 0.6073476 -0.2521945 0.9582453 -0.8266920
row5 -0.27608771 -0.9998615 0.5570443 1.6334328 0.9324440 -0.9493347
col14 col15 col16 col17 col18 col19
row1 -0.3629321 -0.9731777 -0.4889981 0.6009250 0.4533682 -0.1221586
row5 -2.1448605 0.8134957 -0.7873263 0.7047661 -1.0241428 2.3249671
col20
row1 -0.3863065
row5 -0.1300491
> tmp[,c("col6","col20")]
col6 col20
row1 0.8809510 -0.3863065
row2 0.4173557 -1.7271159
row3 -0.8137432 1.0215030
row4 -0.7570826 1.1093287
row5 -0.5911259 -0.1300491
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 0.8809510 -0.3863065
row5 -0.5911259 -0.1300491
>
>
>
>
> 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 49.62175 50.35149 50.29659 49.35743 49.50177 105.7663 49.63795 52.18075
col9 col10 col11 col12 col13 col14 col15 col16
row1 50.02753 49.6179 49.13845 48.88349 49.80738 49.72377 49.65012 50.00474
col17 col18 col19 col20
row1 49.71716 48.79952 49.13153 106.8948
> tmp[,"col10"]
col10
row1 49.61790
row2 30.36300
row3 29.37504
row4 29.57043
row5 50.83732
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 49.62175 50.35149 50.29659 49.35743 49.50177 105.7663 49.63795 52.18075
row5 50.13241 50.89708 48.59257 51.45242 50.51051 106.0149 49.61161 51.28322
col9 col10 col11 col12 col13 col14 col15 col16
row1 50.02753 49.61790 49.13845 48.88349 49.80738 49.72377 49.65012 50.00474
row5 50.78801 50.83732 49.07455 48.31620 52.98431 50.38022 50.22049 51.34030
col17 col18 col19 col20
row1 49.71716 48.79952 49.13153 106.8948
row5 49.36519 51.83669 49.17778 106.5800
> tmp[,c("col6","col20")]
col6 col20
row1 105.76633 106.89484
row2 72.44519 74.31515
row3 75.55225 75.75474
row4 75.69084 75.30655
row5 106.01490 106.58000
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 105.7663 106.8948
row5 106.0149 106.5800
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 105.7663 106.8948
row5 106.0149 106.5800
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] -0.7041254
[2,] 0.3681079
[3,] -0.7318634
[4,] 0.5760692
[5,] -0.7428848
> tmp[,c("col17","col7")]
col17 col7
[1,] 0.1076261 0.8703943
[2,] -0.8886073 -0.6762046
[3,] 0.5694112 -1.3219641
[4,] 1.4575911 -0.1016930
[5,] 0.3104297 1.1465522
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] -0.2941305 -1.3526332
[2,] 1.3971283 -0.8934013
[3,] -0.5082450 0.8540425
[4,] 0.3196274 -0.7202169
[5,] 1.1267499 -0.6638059
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] -0.2941305
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] -0.2941305
[2,] 1.3971283
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
>
>
>
> subBufferedMatrix(tmp,c("row3","row1"),)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row3 0.1040498 -0.358878 0.1962538 0.4313482 -1.317605 -1.1145830 -1.221364
row1 1.4009742 -1.152131 -1.0564635 -1.4008966 -1.891056 0.1031354 -1.339541
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row3 0.3426568 -1.223301 1.2392203 0.6645817 -0.4465972 0.8348860 -0.29955056
row1 1.5631316 -1.230661 -0.7260815 1.4459581 1.2671928 -0.8732249 0.05441497
[,15] [,16] [,17] [,18] [,19] [,20]
row3 -0.3452941 -1.45000442 -0.47774941 0.4450058 -1.333382 0.8890858
row1 0.4692059 -0.01411176 0.01032208 0.9052110 -1.401390 0.3247548
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 1.264157 -0.5124703 -0.640724 -0.04974957 1.617231 -0.3777335 -0.1470923
[,8] [,9] [,10]
row2 0.04025568 -0.6748544 0.525667
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 0.4940739 -1.717746 0.09590532 1.194007 -0.2948474 1.531178 -1.216131
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 1.206278 -0.5735043 0.8118608 -0.4846207 0.1670744 -0.08686942 -0.4368827
[,15] [,16] [,17] [,18] [,19] [,20]
row5 1.743266 2.464394 -1.513125 -0.115528 -0.4221635 -0.6799121
>
>
> 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: 0x7fa4a55025d0>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/Users/biocbuild/bbs-3.11-bioc/meat/BufferedMatrix.Rcheck/tests/BM14b6280acf85"
[2] "/Users/biocbuild/bbs-3.11-bioc/meat/BufferedMatrix.Rcheck/tests/BM14b65dbe394c"
[3] "/Users/biocbuild/bbs-3.11-bioc/meat/BufferedMatrix.Rcheck/tests/BM14b673a3dca8"
[4] "/Users/biocbuild/bbs-3.11-bioc/meat/BufferedMatrix.Rcheck/tests/BM14b6aebd4e8"
[5] "/Users/biocbuild/bbs-3.11-bioc/meat/BufferedMatrix.Rcheck/tests/BM14b6e6d0f2"
[6] "/Users/biocbuild/bbs-3.11-bioc/meat/BufferedMatrix.Rcheck/tests/BM14b6319fc054"
[7] "/Users/biocbuild/bbs-3.11-bioc/meat/BufferedMatrix.Rcheck/tests/BM14b66f0be43f"
[8] "/Users/biocbuild/bbs-3.11-bioc/meat/BufferedMatrix.Rcheck/tests/BM14b675b61d0d"
[9] "/Users/biocbuild/bbs-3.11-bioc/meat/BufferedMatrix.Rcheck/tests/BM14b672d7cdb"
[10] "/Users/biocbuild/bbs-3.11-bioc/meat/BufferedMatrix.Rcheck/tests/BM14b63b60118b"
[11] "/Users/biocbuild/bbs-3.11-bioc/meat/BufferedMatrix.Rcheck/tests/BM14b6201fdb21"
[12] "/Users/biocbuild/bbs-3.11-bioc/meat/BufferedMatrix.Rcheck/tests/BM14b6b6b6401"
[13] "/Users/biocbuild/bbs-3.11-bioc/meat/BufferedMatrix.Rcheck/tests/BM14b637728382"
[14] "/Users/biocbuild/bbs-3.11-bioc/meat/BufferedMatrix.Rcheck/tests/BM14b63f17e83e"
[15] "/Users/biocbuild/bbs-3.11-bioc/meat/BufferedMatrix.Rcheck/tests/BM14b63a905ece"
>
>
> ### 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: 0x7fa4a5506060>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x7fa4a5506060>
Warning message:
In dir.create(new.directory) :
'/Users/biocbuild/bbs-3.11-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x7fa4a5506060>
> rowMedians(tmp)
[1] -0.0207081788 -0.3469873262 0.3752319082 0.0426092981 0.1548055337
[6] 0.2105761227 -0.0641376962 0.1523269401 -0.3407598292 -0.0916483411
[11] 0.1543664863 0.2927161494 0.2930271382 0.0210545049 -0.2747085033
[16] -0.8042021065 0.7331747462 0.2185799135 -0.3424877069 0.0733410663
[21] 0.2789003006 0.1381772349 -0.0209325391 -0.0298720869 -0.2668421104
[26] 0.2570176642 0.0410771239 -0.0177081548 -0.2946625119 -0.6312994236
[31] 0.1457424039 0.1067504090 0.2041112084 0.1494560585 0.1509501293
[36] 0.0620655553 -0.0174312026 -0.3183718683 -0.3535061506 0.1525115413
[41] -0.2697545740 0.0205063107 -0.0697739158 -0.6896096135 -0.0005366124
[46] -0.0537173567 -0.4290730377 0.0999528510 -0.0801009070 0.6943234330
[51] -0.1695584602 0.2962597900 -0.2840330395 -0.3557202115 0.1644932373
[56] 0.0235718166 0.3754583644 0.2973669894 -0.1157105873 -0.2986768199
[61] 0.3724062888 -0.0585207773 -0.0621011655 -0.0426730092 -0.2607455638
[66] -0.6171238720 0.1173240806 0.5618972357 0.7384464961 -0.0908065958
[71] 0.2554273347 -0.1138873066 0.2435501877 0.6954221312 0.3043097538
[76] 0.1276817254 0.0393137836 -0.6198588468 0.4590105656 0.2817084669
[81] 0.0111390754 0.5602926059 -0.3165870084 0.0552335919 0.2963919898
[86] -0.1087640540 0.3548180552 0.3155150737 0.0606290845 -0.2178479911
[91] 0.0215631248 0.1644817187 0.2745582152 0.0336029992 0.0161468634
[96] 0.0644438739 -0.3809231206 0.3570957371 0.4825508474 0.3272790911
[101] 0.7622961536 -0.5026065052 -0.3096791982 -0.2184576492 0.0473566926
[106] 0.0745665439 0.1175810900 0.0581272459 -0.2708212058 0.0638963567
[111] -0.6740189393 -0.5047093386 0.4724330932 -0.3620576250 0.3793684964
[116] -0.9345508889 0.2766940832 0.1263490073 0.0887670617 -0.3285285887
[121] 0.3855720625 -0.1546020972 -0.3305790713 0.1456201593 -0.2528033446
[126] -0.1801984971 0.3868872735 0.0286654838 -0.2833538580 -0.2894003417
[131] 0.2498512905 -0.2148405847 0.0473401957 -0.1374211393 -0.9576366782
[136] -0.3181692464 -0.1890187614 0.3536592286 0.1405203117 0.0833588835
[141] -0.3593347675 -0.1162227200 0.1224585761 0.0285868782 0.0533496337
[146] -0.2074131069 0.0173160428 0.1889430274 0.2492092825 0.5903289501
[151] 0.4830570925 -0.2132320176 -0.0536176486 -0.1075157109 0.0552617938
[156] 0.1547696333 -0.2920175989 -0.2003208073 -0.1186900789 0.0559913595
[161] 0.1424772740 -0.2895432356 0.1052710900 -0.0184228412 -0.3395110050
[166] 0.0722541011 0.3710789435 -0.3117070758 -0.1511406131 0.1490565321
[171] 0.9760023568 -0.3264197974 -0.2760773385 -0.3426301929 -0.0161112448
[176] 0.1037859527 -0.2206965495 -0.2614311548 0.0740854775 0.1207947230
[181] 0.0171894869 -0.2525322751 -0.2002126098 -0.1428370158 0.4250086842
[186] 0.1798592792 -0.0454872860 0.4172672265 -0.2076145609 -0.2296501710
[191] 0.0101043675 0.1577783828 0.2112309169 -0.0768838088 -0.5051947077
[196] 0.1919292181 -0.2870628984 0.3026599665 -0.0845148664 -0.2617285992
[201] 0.3155054900 0.3485726333 -0.3905095413 0.0454547250 0.0875869265
[206] 0.0036154238 0.2363248780 -0.4787272262 -0.1286196921 0.5283901314
[211] -0.1419479686 0.3039423963 0.1977180248 0.3164138950 0.4401902119
[216] 0.3485726456 -0.0746211817 -0.4553690093 0.2891963671 -0.0221311524
[221] 0.1021248544 0.0048024867 -0.1549899178 -0.3012299632 0.0310593239
[226] 0.0793740380 0.4148547951 -0.2785020841 0.3022348532 -0.6790546761
>
> proc.time()
user system elapsed
6.599 16.413 37.922
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
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: 0x7fa35b916ac0>
> .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: 0x7fa35b916ac0>
> .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: 0x7fa35b916ac0>
> .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: 0x7fa35b916ac0>
> 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: 0x7fa35bc00aa0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x7fa35bc00aa0>
> .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: 0x7fa35bc00aa0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x7fa35bc00aa0>
> .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: 0x7fa35bc00aa0>
> 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: 0x7fa35bd00000>
> .Call("R_bm_AddColumn",P)
<pointer: 0x7fa35bd00000>
> .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: 0x7fa35bd00000>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x7fa35bd00000>
> .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: 0x7fa35bd00000>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x7fa35bd00000>
> .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: 0x7fa35bd00000>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x7fa35bd00000>
> .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: 0x7fa35bd00000>
> 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: 0x7fa35be00090>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x7fa35be00090>
> .Call("R_bm_AddColumn",P)
<pointer: 0x7fa35be00090>
> .Call("R_bm_AddColumn",P)
<pointer: 0x7fa35be00090>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile1b667808d2bb" "BufferedMatrixFile1b66b43308e"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile1b667808d2bb" "BufferedMatrixFile1b66b43308e"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x7fa35be003b0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x7fa35be003b0>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x7fa35be003b0>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x7fa35be003b0>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x7fa35be003b0>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x7fa35be003b0>
> .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: 0x7fa35be007c0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x7fa35be007c0>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x7fa35be007c0>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x7fa35be007c0>
> 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: 0x7fa35be00ba0>
> .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: 0x7fa35be00ba0>
> rm(P)
>
> proc.time()
user system elapsed
0.666 0.246 0.865
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
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
>
> Temp <- createBufferedMatrix(100)
> dim(Temp)
[1] 100 0
> buffer.dim(Temp)
[1] 1 1
>
>
> proc.time()
user system elapsed
0.644 0.191 0.777