##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:illuminaio.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings illuminaio_0.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/illuminaio.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘illuminaio/DESCRIPTION’ ... OK
* this is package ‘illuminaio’ version ‘0.42.0’
* 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
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 ... 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 ... 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/illuminaio.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL illuminaio
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘illuminaio’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c 000.init.c -o 000.init.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c des.c -o des.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c local_des.c -o local_des.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o illuminaio.so 000.init.o des.o local_des.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/00LOCK-illuminaio/00new/illuminaio/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** 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 (illuminaio)

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 
  0.211   0.065   0.460 

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 
  1.331   0.124   2.246 

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 
  1.007   0.118   1.745 

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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)
> 
> ## WORKAROUND: Until 'IlluminaDataTestFiles' is updated, 
> ## don't test all of the "Unknowns" fields
> if (  "Unknown.7" %in% names(idat[["Unknowns"]]) &&
+     ! "Unknown.7" %in% names(idat.450k[["Unknowns"]])) {
+   unknowns <- idat[["Unknowns"]]
+   unknowns[["Unknown.6"]] <- NULL
+   unknowns[["Unknown.7"]] <- NULL
+   idat[["Unknowns"]] <- unknowns
+ }
> 
> RUnit::checkEquals(idat, idat.450k)
[1] TRUE
> 
> proc.time()
   user  system elapsed 
  2.173   0.159   3.590 

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 
  1.713   0.146   2.868 

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 
  1.414   0.164   2.437 

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 
  1.218   0.158   2.124 

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 
  1.247   0.167   2.213