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This page was generated on 2023-12-09 12:24:33 -0500 (Sat, 09 Dec 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_64R Under development (unstable) (2023-11-11 r85510) -- "Unsuffered Consequences" 4619
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-11-14 r85524 ucrt) -- "Unsuffered Consequences" 4379
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2023-11-11 r85510) -- "Unsuffered Consequences" 4388
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2023-11-01 r85459) -- "Unsuffered Consequences" 4271
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 146/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
beadarray 2.53.0  (landing page)
Mark Dunning
Snapshot Date: 2023-12-08 14:00:14 -0500 (Fri, 08 Dec 2023)
git_url: https://git.bioconductor.org/packages/beadarray
git_branch: devel
git_last_commit: 45ee237
git_last_commit_date: 2023-10-24 09:36:14 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  

CHECK results for beadarray on kunpeng2


To the developers/maintainers of the beadarray package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/beadarray.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: beadarray
Version: 2.53.0
Command: /home/biocbuild/R/R-4.4-devel-2023.11.02/bin/R CMD check --install=check:beadarray.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library --no-vignettes --timings beadarray_2.53.0.tar.gz
StartedAt: 2023-12-09 06:15:23 -0000 (Sat, 09 Dec 2023)
EndedAt: 2023-12-09 06:20:11 -0000 (Sat, 09 Dec 2023)
EllapsedTime: 287.9 seconds
RetCode: 1
Status:   ERROR  
CheckDir: beadarray.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2023.11.02/bin/R CMD check --install=check:beadarray.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library --no-vignettes --timings beadarray_2.53.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/beadarray.Rcheck’
* using R Under development (unstable) (2023-11-01 r85459)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘beadarray/DESCRIPTION’ ... OK
* this is package ‘beadarray’ version ‘2.53.0’
* 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 (GCC) 10.3.1’
* 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 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) 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 ... 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 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 ... ERROR
Running examples in ‘beadarray-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: imageplot
> ### Title: imageplot for beadLevelData object
> ### Aliases: imageplot
> ### Keywords: hplots
> 
> ### ** Examples
> 
> 
> if(require(beadarrayExampleData)){
+ 
+ data(exampleBLData)
+ 
+ ##By default the first array is plotted, here we plot the 2nd which should give a more interesting example
+ imageplot(exampleBLData, array=2)
+ 
+ }
Loading required package: beadarrayExampleData
* 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 ERROR, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/beadarray.Rcheck/00check.log’
for details.


Installation output

beadarray.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2023.11.02/bin/R CMD INSTALL beadarray
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library’
* installing *source* package ‘beadarray’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-devel/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c BASH.c -o BASH.o
gcc -I"/home/biocbuild/R/R-devel/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c HULK.c -o HULK.o
gcc -I"/home/biocbuild/R/R-devel/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c determiningGridPositions.c -o determiningGridPositions.o
gcc -I"/home/biocbuild/R/R-devel/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c findAllOutliers.c -o findAllOutliers.o
findAllOutliers.c: In function ‘findBeadStatus’:
findAllOutliers.c:196:29: warning: ‘ma’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  196 |   if((inten[k] < (m + *nmads*ma)) && (inten[k] > (m - *nmads*ma))){
      |                       ~~~~~~^~~
findAllOutliers.c:196:53: warning: ‘m’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  196 |   if((inten[k] < (m + *nmads*ma)) && (inten[k] > (m - *nmads*ma))){
      |                                                  ~~~^~~~~~~~~~~~
findAllOutliers.c: In function ‘findAllOutliers’:
findAllOutliers.c:246:13: warning: ‘status’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  246 |  free(status->validInds);
      |       ~~~~~~^~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-devel/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -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 -shared -L/home/biocbuild/R/R-devel/lib -L/usr/local/lib -o beadarray.so BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -L/home/biocbuild/R/R-devel/lib -lR
installing to /home/biocbuild/R/R-4.4-devel-2023.11.02/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)

Tests output


Example timings

beadarray.Rcheck/beadarray-Ex.timings

nameusersystemelapsed
BASH0.0010.0000.001
BASHCompact000
BASHDiffuse000
BASHExtended000
GEO000
GEOtemplate0.0020.0000.002
HULK000
addFeatureData6.0100.2876.480
annotationInterface6.9920.3757.383
backgroundCorrectSingleSection000
beadarrayUsersGuide0.0030.0000.003
boxplot3.7070.1043.823
calculateDetection12.203 0.10812.335
calculateOutlierStats15.706 1.13316.875
class-beadLevelData2.5310.2042.751
class-illuminaChannel0.0020.0000.003
combine3.6950.1433.846
controlProbeDetection11.676 0.15611.856
createTargetsFile000
expressionQCPipeline0.0280.0000.029
generateNeighbours000
getBeadData2.5940.1842.783
identifyControlBeads10.747 1.19112.071
illuminaOutlierMethod2.6120.1042.730