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CHECK report for illuminaio on malbec1

This page was generated on 2018-04-12 13:10:45 -0400 (Thu, 12 Apr 2018).

Package 686/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
illuminaio 0.20.0
Kasper Daniel Hansen
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/illuminaio
Branch: RELEASE_3_6
Last Commit: d226628
Last Changed Date: 2017-10-30 12:39:55 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: illuminaio
Version: 0.20.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings illuminaio_0.20.0.tar.gz
StartedAt: 2018-04-12 00:22:08 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 00:22:44 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 36.1 seconds
RetCode: 0
Status:  OK 
CheckDir: illuminaio.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings illuminaio_0.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/illuminaio.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘illuminaio/DESCRIPTION’ ... OK
* this is package ‘illuminaio’ version ‘0.20.0’
* 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 ‘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
* 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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: OK


Installation output

illuminaio.Rcheck/00install.out

* installing *source* package ‘illuminaio’ ...
** libs
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c des.c -o des.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c local_des.c -o local_des.o
local_des.c: In function ‘decrypt’:
local_des.c:27:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
         fread(sessionKey, 8, 1, f);
         ^
local_des.c:35:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
         fread(data, len, 1, f);
         ^
g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o illuminaio.so des.o local_des.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/illuminaio.Rcheck/illuminaio/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (illuminaio)

Tests output

illuminaio.Rcheck/tests/readBPM.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
  0.200   0.020   0.218 

illuminaio.Rcheck/tests/readIDAT_370k.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
  2.440   0.032   2.568 

illuminaio.Rcheck/tests/readIDAT_370k_gz.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
  2.064   0.088   2.259 

illuminaio.Rcheck/tests/readIDAT_450k.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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)
> RUnit::checkEquals(idat, idat.450k)
[1] TRUE
> 
> proc.time()
   user  system elapsed 
  3.708   0.100   3.866 

illuminaio.Rcheck/tests/readIDAT_450k_gz.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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)
> idatFile2 <- system.file("extdata", "idat", "5723646052_R02C02_Grn.idat.gz",
+                          package = "IlluminaDataTestFiles")
> idat2 <- illuminaio::readIDAT(idatFile2)
> idat2$fileSize <- idat1$fileSize <- NULL
> RUnit::checkEquals(idat1, idat2)
[1] TRUE
> 
> proc.time()
   user  system elapsed 
  3.004   0.100   3.208 

illuminaio.Rcheck/tests/readIDAT_gs_wg6v2.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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)
Warning messages:
1: In read.table(file = file, header = header, sep = sep, quote = quote,  :
  seek on a gzfile connection returned an internal error
2: In read.table(file = file, header = header, sep = sep, quote = quote,  :
  seek on a gzfile connection returned an internal error
> 
> ## 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
Warning message:
In UseMethod("aperm") :
  closing unused connection 3 (/home/biocbuild/bbs-3.6-bioc/R/library/IlluminaDataTestFiles/extdata/gs/4343238080_A_ProbeSummary.txt.gz)
> ## 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 
  2.124   0.048   2.318 

illuminaio.Rcheck/tests/readIDAT_ht12v4.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
  1.532   0.032   1.624 

illuminaio.Rcheck/tests/readIDAT_wg6v2.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
  1.084   0.048   1.129 

Example timings

illuminaio.Rcheck/illuminaio-Ex.timings

nameusersystemelapsed
readIDAT0.8280.0360.948