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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:beadarray.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings beadarray_2.59.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/beadarray.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘beadarray/DESCRIPTION’ ... OK
* this is package ‘beadarray’ version ‘2.59.0’
* 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 ‘beadarray’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘hexbin’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  ‘BeadDataPackR:::combineFiles’ ‘BeadDataPackR:::readHeader’
  ‘Biobase:::assayDataStorageMode’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .Call("roundLocsFileValues", ..., PACKAGE = "BeadDataPackR")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
combinedControlPlot: no visible binding for global variable ‘Negative’
createGEOMeta: no visible binding for global variable ‘metaTemplate’
expressionQCPipeline: no visible global function definition for
  ‘openPage’
expressionQCPipeline: no visible global function definition for
  ‘hwrite’
expressionQCPipeline: no visible global function definition for
  ‘hwriteImage’
expressionQCPipeline: no visible global function definition for
  ‘closePage’
getPlatformSigs: no visible global function definition for
  ‘lumiHumanIDMapping_dbconn’
getPlatformSigs: no visible global function definition for
  ‘dbListTables’
getPlatformSigs: no visible global function definition for
  ‘dbListFields’
getPlatformSigs: no visible global function definition for ‘dbGetQuery’
getPlatformSigs: no visible global function definition for
  ‘lumiMouseIDMapping_dbconn’
getPlatformSigs: no visible global function definition for
  ‘lumiRatIDMapping_dbconn’
imageplot: no visible binding for global variable ‘Var1’
imageplot: no visible binding for global variable ‘Var2’
imageplot: no visible binding for global variable ‘value’
makeReport: no visible binding for global variable ‘Nozzle.R1’
makeReport: no visible binding for global variable ‘ggbio’
makeReport: no visible global function definition for ‘newCustomReport’
makeReport: no visible global function definition for ‘newSection’
makeReport: no visible global function definition for ‘newTable’
makeReport: no visible global function definition for ‘newParagraph’
makeReport: no visible global function definition for ‘addTo’
makeReport: no visible global function definition for ‘autoplot’
makeReport: no visible global function definition for ‘plotIdeogram’
makeReport: no visible global function definition for ‘tracks’
makeReport: no visible global function definition for ‘newFigure’
makeReport: no visible binding for global variable ‘IMAGE.TYPE.RASTER’
makeReport: no visible binding for global variable ‘PROTECTION.PUBLIC’
makeReport: no visible binding for global variable ‘value’
makeReport: no visible global function definition for ‘writeReport’
maplots: no visible binding for global variable ‘value.1’
maplots: no visible binding for global variable ‘value’
normaliseIllumina: no visible global function definition for ‘lumiT’
normaliseIllumina: no visible global function definition for
  ‘normalize.qspline’
normaliseIllumina: no visible global function definition for ‘vsn2’
plotBeadLocations2: no visible global function definition for ‘qplot’
plotBeadLocations2: no visible global function definition for ‘opts’
plotBeadLocations2: no visible global function definition for
  ‘theme_blank’
plotProbe: no visible global function definition for ‘autoplot’
plotProbe: no visible binding for global variable ‘genesymbol’
plotProbe: no visible global function definition for ‘tracks’
plotProbe: no visible binding for global variable ‘PROBEQUALITY’
rankInvariantNormalise: no visible global function definition for
  ‘normalize.invariantset’
suggestAnnotation: no visible binding for global variable
  ‘platformSigs’
suggestAnnotation_Vector: no visible binding for global variable
  ‘platformSigs’
[,ExpressionSetIllumina-ANY: no visible global function definition for
  ‘assayDataEnvLock’
boxplot,ExpressionSetIllumina: no visible binding for global variable
  ‘Var2’
boxplot,ExpressionSetIllumina: no visible binding for global variable
  ‘value’
plotMA,ExpressionSetIllumina: no visible binding for global variable
  ‘value.1’
plotMA,ExpressionSetIllumina: no visible binding for global variable
  ‘value’
Undefined global functions or variables:
  IMAGE.TYPE.RASTER Negative Nozzle.R1 PROBEQUALITY PROTECTION.PUBLIC
  Var1 Var2 addTo assayDataEnvLock autoplot closePage dbGetQuery
  dbListFields dbListTables genesymbol ggbio hwrite hwriteImage
  lumiHumanIDMapping_dbconn lumiMouseIDMapping_dbconn
  lumiRatIDMapping_dbconn lumiT metaTemplate newCustomReport newFigure
  newParagraph newSection newTable normalize.invariantset
  normalize.qspline openPage opts platformSigs plotIdeogram qplot
  theme_blank tracks value value.1 vsn2 writeReport
* checking Rd files ... NOTE
checkRd: (-1) createTargetsFile.Rd:49: Lost braces
    49 | code{metricsflag}: This gives the key word that can be used to identify metrics files.  
       |     ^
checkRd: (-1) readBeadSummaryData.Rd:70: Escaped LaTeX specials: \_
checkRd: (-1) readBeadSummaryData.Rd:71: Escaped LaTeX specials: \_ \_
checkRd: (-1) readBeadSummaryData.Rd:76: Escaped LaTeX specials: \_ \_
checkRd: (-1) sampleSheet.Rd:26: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'class-ExpressionSetIllumina.Rd':
  ‘[Biobase:class.eSet]{eSet}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
squeezedVarOutlierMethod 46.249  0.204  46.457
summarize                20.435  0.935  21.372
limmaDE                  13.972  0.113  14.089
normaliseIllumina        12.726  0.228  12.956
calculateOutlierStats    10.516  0.650  11.166
controlProbeDetection    10.369  0.089  10.463
outlierplot               9.912  0.279  10.191
calculateDetection        9.817  0.159   9.976
insertSectionData         9.035  0.357   9.393
identifyControlBeads      9.149  0.036   9.188
makeQCTable               8.761  0.394   9.156
poscontPlot               8.221  0.130   8.352
annotationInterface       6.452  0.555   7.011
quickSummary              6.302  0.123   6.427
imageplot                 6.163  0.088   6.253
addFeatureData            5.542  0.259   5.813
showArrayMask             4.971  0.114   5.086
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘ImageProcessing.Rmd’ using rmarkdown
--- finished re-building ‘ImageProcessing.Rmd’

--- re-building ‘beadarray.Rmd’ using rmarkdown
--- finished re-building ‘beadarray.Rmd’

--- re-building ‘beadlevel.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/beadarray.Rcheck/vign_test/beadarray/vignettes/beadlevel_files/figure-html/unnamed-chunk-6-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/beadarray.Rcheck/vign_test/beadarray/vignettes/beadlevel_files/figure-html/unnamed-chunk-7-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/beadarray.Rcheck/vign_test/beadarray/vignettes/beadlevel_files/figure-html/unnamed-chunk-13-1.png" but not available.
--- finished re-building ‘beadlevel.Rmd’

--- re-building ‘beadsummary.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/beadarray.Rcheck/vign_test/beadarray/vignettes/beadsummary_files/figure-html/unnamed-chunk-8-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/beadarray.Rcheck/vign_test/beadarray/vignettes/beadsummary_files/figure-html/unnamed-chunk-9-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/beadarray.Rcheck/vign_test/beadarray/vignettes/beadsummary_files/figure-html/unnamed-chunk-10-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/beadarray.Rcheck/vign_test/beadarray/vignettes/beadsummary_files/figure-html/unnamed-chunk-11-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/beadarray.Rcheck/vign_test/beadarray/vignettes/beadsummary_files/figure-html/unnamed-chunk-13-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/beadarray.Rcheck/vign_test/beadarray/vignettes/beadsummary_files/figure-html/unnamed-chunk-14-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/beadarray.Rcheck/vign_test/beadarray/vignettes/beadsummary_files/figure-html/unnamed-chunk-16-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/beadarray.Rcheck/vign_test/beadarray/vignettes/beadsummary_files/figure-html/unnamed-chunk-17-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/beadarray.Rcheck/vign_test/beadarray/vignettes/beadsummary_files/figure-html/unnamed-chunk-17-2.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/beadarray.Rcheck/vign_test/beadarray/vignettes/beadsummary_files/figure-html/unnamed-chunk-17-3.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/beadarray.Rcheck/vign_test/beadarray/vignettes/beadsummary_files/figure-html/unnamed-chunk-18-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/beadarray.Rcheck/vign_test/beadarray/vignettes/beadsummary_files/figure-html/unnamed-chunk-23-1.png" but not available.
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE33nnn/GSE33126/matrix/GSE33126_series_matrix.txt.gz'

Quitting from beadsummary.Rmd:426-434 [unnamed-chunk-32]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `download.file()`:
! cannot open URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE33nnn/GSE33126/matrix/GSE33126_series_matrix.txt.gz'
---
Backtrace:
    ▆
 1. └─utils::download.file(paste(url, filenm, sep = ""), destfile = filenm)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'beadsummary.Rmd' failed with diagnostics:
cannot open URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE33nnn/GSE33126/matrix/GSE33126_series_matrix.txt.gz'
--- failed re-building ‘beadsummary.Rmd’

SUMMARY: processing the following file failed:
  ‘beadsummary.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 7 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/beadarray.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL beadarray
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘beadarray’ ...
** this is package ‘beadarray’ version ‘2.59.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c BASH.c -o BASH.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c HULK.c -o HULK.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c determiningGridPositions.c -o determiningGridPositions.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c findAllOutliers.c -o findAllOutliers.o
findAllOutliers.c: In function ‘findBeadStatus’:
findAllOutliers.c:196:35: warning: ‘m’ may be used uninitialized [-Wmaybe-uninitialized]
  196 |                 if((inten[k] < (m + *nmads*ma)) && (inten[k] > (m - *nmads*ma))){
      |                                ~~~^~~~~~~~~~~~
findAllOutliers.c:155:16: note: ‘m’ was declared here
  155 |         double m, ma;
      |                ^
findAllOutliers.c:189:15: warning: ‘ma’ may be used uninitialized [-Wmaybe-uninitialized]
  189 |             if(ma==0) {
      |               ^
findAllOutliers.c:155:19: note: ‘ma’ was declared here
  155 |         double m, ma;
      |                   ^~
findAllOutliers.c: In function ‘findAllOutliers’:
findAllOutliers.c:246:20: warning: ‘status’ may be used uninitialized [-Wmaybe-uninitialized]
  246 |         free(status->validInds);
      |              ~~~~~~^~~~~~~~~~~
findAllOutliers.c:226:27: note: ‘status’ was declared here
  226 |         beadStatusStruct *status;
      |                           ^~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c imageProcessing.c -o imageProcessing.o
imageProcessing.c: In function ‘illuminaBackground’:
imageProcessing.c:88: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
   88 |     #pragma omp parallel shared(nthreads, nbeads, imageHeight, pixelMatrix, coords) private(tid, start, end)
      | 
imageProcessing.c: In function ‘medianBackground’:
imageProcessing.c:135: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  135 |     #pragma omp parallel shared(nthreads, nbeads, imageHeight, pixelMatrix, coords) private(tid, start, end)
      | 
imageProcessing.c: In function ‘illuminaSharpen’:
imageProcessing.c:244: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  244 |     #pragma omp parallel for private(i, j) shared(sharpened) num_threads(2)
      | 
imageProcessing.c:251: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  251 |     #pragma omp parallel for private(i, j, sum) shared(sharpened) num_threads(2)
      | 
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o beadarray.so BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-beadarray/00new/beadarray/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (beadarray)