Kasper Daniel Hansen
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/illuminaio |
| Branch: RELEASE_3_11 |
| Last Commit: d3faefa |
| Last Changed Date: 2020-04-27 14:31:59 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:52 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE illuminaio PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 864/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| illuminaio 0.30.0 Kasper Daniel Hansen
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: illuminaio |
| Version: 0.30.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:illuminaio.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings illuminaio_0.30.0.tar.gz |
| StartedAt: 2020-10-17 05:10:20 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 05:11:39 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 79.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: illuminaio.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:illuminaio.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings illuminaio_0.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/illuminaio.Rcheck' * using R version 4.0.3 (2020-10-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'illuminaio/DESCRIPTION' ... OK * this is package 'illuminaio' version '0.30.0' * 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 whether package 'illuminaio' 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 ... OK * 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 for i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/illuminaio/libs/i386/illuminaio.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/illuminaio/libs/x64/illuminaio.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'readBPM.R' Running 'readIDAT_370k.R' Running 'readIDAT_370k_gz.R' Running 'readIDAT_450k.R' Running 'readIDAT_450k_gz.R' Running 'readIDAT_gs_wg6v2.R' Running 'readIDAT_ht12v4.R' Running 'readIDAT_wg6v2.R' OK ** running tests for arch 'x64' ... Running 'readBPM.R' Running 'readIDAT_370k.R' Running 'readIDAT_370k_gz.R' Running 'readIDAT_450k.R' Running 'readIDAT_450k_gz.R' Running 'readIDAT_gs_wg6v2.R' Running 'readIDAT_ht12v4.R' Running 'readIDAT_wg6v2.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: 1 NOTE See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/illuminaio.Rcheck/00check.log' for details.
illuminaio.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/illuminaio_0.30.0.tar.gz && rm -rf illuminaio.buildbin-libdir && mkdir illuminaio.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=illuminaio.buildbin-libdir illuminaio_0.30.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL illuminaio_0.30.0.zip && rm illuminaio_0.30.0.tar.gz illuminaio_0.30.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 30632 100 30632 0 0 115k 0 --:--:-- --:--:-- --:--:-- 118k
install for i386
* installing *source* package 'illuminaio' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c 000.init.c -o 000.init.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c des.c -o des.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c local_des.c -o local_des.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o illuminaio.dll tmp.def 000.init.o des.o local_des.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/illuminaio.buildbin-libdir/00LOCK-illuminaio/00new/illuminaio/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'illuminaio'
finding HTML links ... done
readBGX html
readBPM html
readIDAT html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'illuminaio' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c 000.init.c -o 000.init.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c des.c -o des.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c local_des.c -o local_des.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o illuminaio.dll tmp.def 000.init.o des.o local_des.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/illuminaio.buildbin-libdir/illuminaio/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'illuminaio' as illuminaio_0.30.0.zip
* DONE (illuminaio)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'illuminaio' successfully unpacked and MD5 sums checked
|
illuminaio.Rcheck/tests_i386/readBPM.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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.
> ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> ## System tests for readBPM()
> ##
> ## Data is automatically downloaded from Illumina (e.g. [1]), if missing.
> ##
> ## NOTE: These tests will only run if '_R_CHECK_FULL_' is set, i.e.
> ## they won't run on Bioconductor or CRAN servers.
> ##
> ## REFERENCES:
> ## [1] http://support.illumina.com/downloads/infinium_bovineld_beadchip_product_files.ilmn
> ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> if (FALSE && Sys.getenv("_R_CHECK_FULL_") != "") {
+
+ ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+ ## Utility functions
+ ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+ getIlluminaAnnotationFile <- function(chipType, filename, force=FALSE) {
+ # Share data files across architectures, e.g. tests_i386 and tests_x64.
+ rootPath <- "../annotationData,illuminaio,tests"
+ path <- file.path(rootPath, "chipTypes", chipType)
+ if (!file_test("-d", path)) dir.create(path, recursive=TRUE)
+ pathname <- file.path(path, filename)
+
+ # Already downloaded?
+ if (!force && file_test("-f", pathname)) return(pathname)
+
+ # Download from Illumina
+ urlRoot <- "http://supportres.illumina.com/documents/downloads/productfiles"
+ url <- file.path(urlRoot, chipType, filename)
+ download.file(url, destfile=pathname, mode="wb")
+ if (!file_test("-f", pathname)) stop("Failed to download file: ", url)
+
+ pathname
+ } # getIlluminaAnnotationFile()
+
+
+ ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+ ## Tests
+ ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+ ## pathname <- getIlluminaAnnotationFile("bovineld", "bovineld_c.bpm")
+
+ path <- "annotationData/chipTypes/HumanMethylation450"
+ filename <- "humanmethylation450_15017482_v-1-2.bpm"
+ pathname <- file.path(path,filename)
+ data <- illuminaio::readBPM(pathname)
+ str(data)
+
+ } # if (Sys.getenv("_R_CHECK_FULL_") != "")
>
> proc.time()
user system elapsed
0.28 0.07 0.32
|
illuminaio.Rcheck/tests_x64/readBPM.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.
> ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> ## System tests for readBPM()
> ##
> ## Data is automatically downloaded from Illumina (e.g. [1]), if missing.
> ##
> ## NOTE: These tests will only run if '_R_CHECK_FULL_' is set, i.e.
> ## they won't run on Bioconductor or CRAN servers.
> ##
> ## REFERENCES:
> ## [1] http://support.illumina.com/downloads/infinium_bovineld_beadchip_product_files.ilmn
> ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> if (FALSE && Sys.getenv("_R_CHECK_FULL_") != "") {
+
+ ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+ ## Utility functions
+ ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+ getIlluminaAnnotationFile <- function(chipType, filename, force=FALSE) {
+ # Share data files across architectures, e.g. tests_i386 and tests_x64.
+ rootPath <- "../annotationData,illuminaio,tests"
+ path <- file.path(rootPath, "chipTypes", chipType)
+ if (!file_test("-d", path)) dir.create(path, recursive=TRUE)
+ pathname <- file.path(path, filename)
+
+ # Already downloaded?
+ if (!force && file_test("-f", pathname)) return(pathname)
+
+ # Download from Illumina
+ urlRoot <- "http://supportres.illumina.com/documents/downloads/productfiles"
+ url <- file.path(urlRoot, chipType, filename)
+ download.file(url, destfile=pathname, mode="wb")
+ if (!file_test("-f", pathname)) stop("Failed to download file: ", url)
+
+ pathname
+ } # getIlluminaAnnotationFile()
+
+
+ ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+ ## Tests
+ ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+ ## pathname <- getIlluminaAnnotationFile("bovineld", "bovineld_c.bpm")
+
+ path <- "annotationData/chipTypes/HumanMethylation450"
+ filename <- "humanmethylation450_15017482_v-1-2.bpm"
+ pathname <- file.path(path,filename)
+ data <- illuminaio::readBPM(pathname)
+ str(data)
+
+ } # if (Sys.getenv("_R_CHECK_FULL_") != "")
>
> proc.time()
user system elapsed
0.26 0.04 0.35
|
|
illuminaio.Rcheck/tests_i386/readIDAT_370k.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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(illuminaio)
> library(IlluminaDataTestFiles)
>
> load(file.path(path.package("IlluminaDataTestFiles"), "extdata", "testData", "idat.370k.rda"))
> idatFile <- system.file("extdata", "idat", "4019585376_B_Red.idat",
+ package = "IlluminaDataTestFiles")
> idat <- illuminaio::readIDAT(idatFile)
> ## FIXME: IlluminaDataTestFiles needs to be updated according
> ## to 'RunInfo' bug fix in illuminaio v0.11.2.
> if (packageVersion("illuminaio") > "0.11.1") idat$RunInfo[-(1:2),] <- NA
> RUnit::checkEquals(idat, idat.370k)
[1] TRUE
>
> proc.time()
user system elapsed
2.06 0.12 2.48
|
illuminaio.Rcheck/tests_x64/readIDAT_370k.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(illuminaio)
> library(IlluminaDataTestFiles)
>
> load(file.path(path.package("IlluminaDataTestFiles"), "extdata", "testData", "idat.370k.rda"))
> idatFile <- system.file("extdata", "idat", "4019585376_B_Red.idat",
+ package = "IlluminaDataTestFiles")
> idat <- illuminaio::readIDAT(idatFile)
> ## FIXME: IlluminaDataTestFiles needs to be updated according
> ## to 'RunInfo' bug fix in illuminaio v0.11.2.
> if (packageVersion("illuminaio") > "0.11.1") idat$RunInfo[-(1:2),] <- NA
> RUnit::checkEquals(idat, idat.370k)
[1] TRUE
>
> proc.time()
user system elapsed
1.84 0.15 2.00
|
|
illuminaio.Rcheck/tests_i386/readIDAT_370k_gz.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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(illuminaio)
> library(IlluminaDataTestFiles)
>
> idatFile1 <- system.file("extdata", "idat", "4019585376_B_Red.idat",
+ package = "IlluminaDataTestFiles")
> idat1 <- illuminaio::readIDAT(idatFile1)
> idatFile2 <- system.file("extdata", "idat", "4019585376_B_Red.idat.gz",
+ package = "IlluminaDataTestFiles")
> idat2 <- illuminaio::readIDAT(idatFile2)
> idat2$fileSize <- idat1$fileSize <- NULL
> RUnit::checkEquals(idat1, idat2)
[1] TRUE
>
> proc.time()
user system elapsed
1.81 0.07 2.87
|
illuminaio.Rcheck/tests_x64/readIDAT_370k_gz.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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(illuminaio)
> library(IlluminaDataTestFiles)
>
> idatFile1 <- system.file("extdata", "idat", "4019585376_B_Red.idat",
+ package = "IlluminaDataTestFiles")
> idat1 <- illuminaio::readIDAT(idatFile1)
> idatFile2 <- system.file("extdata", "idat", "4019585376_B_Red.idat.gz",
+ package = "IlluminaDataTestFiles")
> idat2 <- illuminaio::readIDAT(idatFile2)
> idat2$fileSize <- idat1$fileSize <- NULL
> RUnit::checkEquals(idat1, idat2)
[1] TRUE
>
> proc.time()
user system elapsed
1.42 0.09 1.50
|
|
illuminaio.Rcheck/tests_i386/readIDAT_450k.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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(IlluminaDataTestFiles)
>
> load(file.path(path.package("IlluminaDataTestFiles"), "extdata", "testData", "idat.450k.rda"))
> idatFile <- system.file("extdata", "idat", "5723646052_R02C02_Grn.idat",
+ package = "IlluminaDataTestFiles")
> idat <- illuminaio::readIDAT(idatFile)
Warning message:
In readChar(con, nchars = n) : truncating string with embedded nuls
> RUnit::checkEquals(idat, idat.450k)
[1] TRUE
>
> proc.time()
user system elapsed
3.73 0.15 6.14
|
illuminaio.Rcheck/tests_x64/readIDAT_450k.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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(IlluminaDataTestFiles)
>
> load(file.path(path.package("IlluminaDataTestFiles"), "extdata", "testData", "idat.450k.rda"))
> idatFile <- system.file("extdata", "idat", "5723646052_R02C02_Grn.idat",
+ package = "IlluminaDataTestFiles")
> idat <- illuminaio::readIDAT(idatFile)
Warning message:
In readChar(con, nchars = n) : truncating string with embedded nuls
> RUnit::checkEquals(idat, idat.450k)
[1] TRUE
>
> proc.time()
user system elapsed
2.59 0.12 2.70
|
|
illuminaio.Rcheck/tests_i386/readIDAT_450k_gz.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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(illuminaio)
> library(IlluminaDataTestFiles)
>
> idatFile1 <- system.file("extdata", "idat", "5723646052_R02C02_Grn.idat",
+ package = "IlluminaDataTestFiles")
> idat1 <- illuminaio::readIDAT(idatFile1)
Warning message:
In readChar(con, nchars = n) : truncating string with embedded nuls
> idatFile2 <- system.file("extdata", "idat", "5723646052_R02C02_Grn.idat.gz",
+ package = "IlluminaDataTestFiles")
> idat2 <- illuminaio::readIDAT(idatFile2)
Warning message:
In readChar(con, nchars = n) : truncating string with embedded nuls
> idat2$fileSize <- idat1$fileSize <- NULL
> RUnit::checkEquals(idat1, idat2)
[1] TRUE
>
> proc.time()
user system elapsed
2.46 0.20 4.65
|
illuminaio.Rcheck/tests_x64/readIDAT_450k_gz.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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(illuminaio)
> library(IlluminaDataTestFiles)
>
> idatFile1 <- system.file("extdata", "idat", "5723646052_R02C02_Grn.idat",
+ package = "IlluminaDataTestFiles")
> idat1 <- illuminaio::readIDAT(idatFile1)
Warning message:
In readChar(con, nchars = n) : truncating string with embedded nuls
> idatFile2 <- system.file("extdata", "idat", "5723646052_R02C02_Grn.idat.gz",
+ package = "IlluminaDataTestFiles")
> idat2 <- illuminaio::readIDAT(idatFile2)
Warning message:
In readChar(con, nchars = n) : truncating string with embedded nuls
> idat2$fileSize <- idat1$fileSize <- NULL
> RUnit::checkEquals(idat1, idat2)
[1] TRUE
>
> proc.time()
user system elapsed
2.03 0.09 2.11
|
|
illuminaio.Rcheck/tests_i386/readIDAT_gs_wg6v2.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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(illuminaio)
> library(IlluminaDataTestFiles)
>
> idatFile <- system.file("extdata", "idat", "4343238080_A_Grn.idat", package = "IlluminaDataTestFiles")
> idatData <- readIDAT(idatFile)$Quants
> gsFile <- system.file("extdata", "gs", "4343238080_A_ProbeSummary.txt.gz", package = "IlluminaDataTestFiles")
> gStudio <- read.delim(gzfile(gsFile, open = "r"), sep = "\t", header = TRUE)
>
> ## not all probes are present in GenomeStudio output, so only select those that are
> idatData <- idatData[which(idatData[,"CodesBinData"] %in% gStudio[,"ProbeID"]),]
> ## the orders are also different (numeric vs alphabetical)
> gStudio <- gStudio[match(idatData[,"CodesBinData"], gStudio[,"ProbeID"]),]
> # check each value in GenomeStudio output
> ## there are some rounding differences, so we allow slight differences
>
> ## summarised bead intensities
> RUnit::checkEqualsNumeric(idatData[, "MeanBinData"], gStudio[, 3], tolerance = 10e-7)
[1] TRUE
> ## number of beads
> RUnit::checkEquals(idatData[, "NumGoodBeadsBinData"], gStudio[, 5])
[1] TRUE
> ## standard errors
> RUnit::checkEqualsNumeric(idatData[, "DevBinData"] / sqrt(idatData[, "NumGoodBeadsBinData"]), gStudio[, 4], tolerance = 10e-7)
[1] TRUE
>
> proc.time()
user system elapsed
1.59 0.21 4.42
|
illuminaio.Rcheck/tests_x64/readIDAT_gs_wg6v2.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(illuminaio)
> library(IlluminaDataTestFiles)
>
> idatFile <- system.file("extdata", "idat", "4343238080_A_Grn.idat", package = "IlluminaDataTestFiles")
> idatData <- readIDAT(idatFile)$Quants
> gsFile <- system.file("extdata", "gs", "4343238080_A_ProbeSummary.txt.gz", package = "IlluminaDataTestFiles")
> gStudio <- read.delim(gzfile(gsFile, open = "r"), sep = "\t", header = TRUE)
>
> ## not all probes are present in GenomeStudio output, so only select those that are
> idatData <- idatData[which(idatData[,"CodesBinData"] %in% gStudio[,"ProbeID"]),]
> ## the orders are also different (numeric vs alphabetical)
> gStudio <- gStudio[match(idatData[,"CodesBinData"], gStudio[,"ProbeID"]),]
> # check each value in GenomeStudio output
> ## there are some rounding differences, so we allow slight differences
>
> ## summarised bead intensities
> RUnit::checkEqualsNumeric(idatData[, "MeanBinData"], gStudio[, 3], tolerance = 10e-7)
[1] TRUE
> ## number of beads
> RUnit::checkEquals(idatData[, "NumGoodBeadsBinData"], gStudio[, 5])
[1] TRUE
> ## standard errors
> RUnit::checkEqualsNumeric(idatData[, "DevBinData"] / sqrt(idatData[, "NumGoodBeadsBinData"]), gStudio[, 4], tolerance = 10e-7)
[1] TRUE
>
> proc.time()
user system elapsed
1.62 0.06 2.70
|
|
illuminaio.Rcheck/tests_i386/readIDAT_ht12v4.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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(illuminaio)
> library(IlluminaDataTestFiles)
>
> load(file.path(path.package("IlluminaDataTestFiles"), "extdata", "testData", "idat.ht12v4.rda"))
> idatFile <- system.file("extdata", "idat", "6016741005_A_Grn.idat",
+ package = "IlluminaDataTestFiles")
> idat <- illuminaio::readIDAT(idatFile)
> RUnit::checkEquals(idat, idat.ht12v4)
[1] TRUE
>
> proc.time()
user system elapsed
1.57 0.20 4.07
|
illuminaio.Rcheck/tests_x64/readIDAT_ht12v4.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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(illuminaio)
> library(IlluminaDataTestFiles)
>
> load(file.path(path.package("IlluminaDataTestFiles"), "extdata", "testData", "idat.ht12v4.rda"))
> idatFile <- system.file("extdata", "idat", "6016741005_A_Grn.idat",
+ package = "IlluminaDataTestFiles")
> idat <- illuminaio::readIDAT(idatFile)
> RUnit::checkEquals(idat, idat.ht12v4)
[1] TRUE
>
> proc.time()
user system elapsed
1.06 0.10 2.00
|
|
illuminaio.Rcheck/tests_i386/readIDAT_wg6v2.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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(illuminaio)
> library(IlluminaDataTestFiles)
>
> load(file.path(path.package("IlluminaDataTestFiles"), "extdata", "testData", "idat.wg6v2.rda"))
> idatFile <- system.file("extdata", "idat", "4343238080_A_Grn.idat",
+ package = "IlluminaDataTestFiles")
> idat <- illuminaio::readIDAT(idatFile)
> RUnit::checkEquals(idat, idat.wg6v2)
[1] TRUE
>
> proc.time()
user system elapsed
1.56 0.15 2.75
|
illuminaio.Rcheck/tests_x64/readIDAT_wg6v2.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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(illuminaio)
> library(IlluminaDataTestFiles)
>
> load(file.path(path.package("IlluminaDataTestFiles"), "extdata", "testData", "idat.wg6v2.rda"))
> idatFile <- system.file("extdata", "idat", "4343238080_A_Grn.idat",
+ package = "IlluminaDataTestFiles")
> idat <- illuminaio::readIDAT(idatFile)
> RUnit::checkEquals(idat, idat.wg6v2)
[1] TRUE
>
> proc.time()
user system elapsed
0.93 0.17 1.39
|
|
illuminaio.Rcheck/examples_i386/illuminaio-Ex.timings
|
illuminaio.Rcheck/examples_x64/illuminaio-Ex.timings
|