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This page was generated on 2024-05-07 11:37:27 -0400 (Tue, 07 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4485
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4258
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4470
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4480
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 2097/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SubCellBarCode 1.20.0  (landing page)
Taner Arslan
Snapshot Date: 2024-05-06 14:00:20 -0400 (Mon, 06 May 2024)
git_url: https://git.bioconductor.org/packages/SubCellBarCode
git_branch: RELEASE_3_19
git_last_commit: e78663e
git_last_commit_date: 2024-04-30 11:14:57 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 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
lconwaymacOS 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    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for SubCellBarCode on nebbiolo1


To the developers/maintainers of the SubCellBarCode package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SubCellBarCode.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.

raw results


Summary

Package: SubCellBarCode
Version: 1.20.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:SubCellBarCode.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings SubCellBarCode_1.20.0.tar.gz
StartedAt: 2024-05-07 04:09:42 -0400 (Tue, 07 May 2024)
EndedAt: 2024-05-07 04:17:57 -0400 (Tue, 07 May 2024)
EllapsedTime: 495.1 seconds
RetCode: 0
Status:   OK  
CheckDir: SubCellBarCode.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:SubCellBarCode.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings SubCellBarCode_1.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/SubCellBarCode.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘SubCellBarCode/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SubCellBarCode’ version ‘1.20.0’
* package encoding: UTF-8
* 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 ‘SubCellBarCode’ 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 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 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 ... NOTE
calculateCoveredProtein: no visible binding for global variable
  ‘Compartments’
calculateCoveredProtein: no visible binding for global variable
  ‘ProteinCoverage’
candidateRelocatedProteins: no visible binding for global variable
  ‘Pearson.Corr’
markerQualityControl: no visible binding for global variable
  ‘Correlation’
markerQualityControl: no visible binding for global variable ‘Pearson’
markerQualityControl: no visible binding for global variable ‘Spearman’
plotBarcode: no visible binding for global variable ‘Level’
plotBarcode: no visible binding for global variable ‘Probability’
plotBarcode: no visible binding for global variable ‘Locs’
plotMultipleProtein: no visible binding for global variable
  ‘Neighborhood’
plotMultipleProtein: no visible binding for global variable ‘Count’
plotMultipleProtein: no visible binding for global variable
  ‘Compartment’
Undefined global functions or variables:
  Compartment Compartments Correlation Count Level Locs Neighborhood
  Pearson Pearson.Corr Probability ProteinCoverage Spearman
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                               user system elapsed
applyThresholdCompartment    14.460  0.380  14.840
applyThresholdNeighborhood   11.558  0.228  11.787
computeThresholdCompartment  11.301  0.092  11.394
computeThresholdNeighborhood 10.880  0.160  11.040
svmExternalData               9.293  0.028   9.321
svmClassification             7.787  0.048   7.834
candidateRelocatedProteins    6.212  0.060   6.272
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/SubCellBarCode.Rcheck/00check.log’
for details.


Installation output

SubCellBarCode.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL SubCellBarCode
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘SubCellBarCode’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SubCellBarCode)

Tests output


Example timings

SubCellBarCode.Rcheck/SubCellBarCode-Ex.timings

nameusersystemelapsed
applyThresholdCompartment14.46 0.3814.84
applyThresholdNeighborhood11.558 0.22811.787
calRowMean0.0050.0000.005
calculateCoveredProtein0.1190.0000.119
candidateRelocatedProteins6.2120.0606.272
compareCls0.0090.0040.014
computeThresholdCompartment11.301 0.09211.394
computeThresholdNeighborhood10.88 0.1611.04
convert2symbol0.0000.0010.000
hcc827Ctrl0.0000.0030.003
hcc827CtrlPSMCount0.0030.0030.006
hcc827GEF0.0020.0000.002
hcc827GEFClass0.0020.0000.001
hcc827GefPSMCount0.0010.0000.001
hcc827exon0.0030.0000.002
loadData0.0010.0000.000
markerQualityControl0.3890.0000.389
mergeCls0.0040.0000.004
mergeProbability0.0040.0000.003
plotBarcode0.4930.0110.504
plotMultipleProtein0.2380.0040.242
replacePrediction0.0030.0000.004
sankeyPlot0.0170.0080.025
sumProbability0.0040.0000.004
svmClassification7.7870.0487.834
svmExternalData9.2930.0289.321
tsneVisualization0.1730.0040.177