Back to Multiple platform build/check report for BioC 3.16:   simplified   long
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2023-04-12 11:05:21 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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

CHECK results for SubCellBarCode on nebbiolo2


To the developers/maintainers of the SubCellBarCode package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1988/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SubCellBarCode 1.14.0  (landing page)
Taner Arslan
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/SubCellBarCode
git_branch: RELEASE_3_16
git_last_commit: 4fdc616
git_last_commit_date: 2022-11-01 11:19:56 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: SubCellBarCode
Version: 1.14.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:SubCellBarCode.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings SubCellBarCode_1.14.0.tar.gz
StartedAt: 2023-04-11 00:24:05 -0400 (Tue, 11 Apr 2023)
EndedAt: 2023-04-11 00:31:55 -0400 (Tue, 11 Apr 2023)
EllapsedTime: 469.3 seconds
RetCode: 0
Status:   OK  
CheckDir: SubCellBarCode.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:SubCellBarCode.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings SubCellBarCode_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/SubCellBarCode.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘SubCellBarCode/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SubCellBarCode’ version ‘1.14.0’
* 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 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 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    13.394  0.292  13.686
applyThresholdNeighborhood   10.995  0.112  11.107
computeThresholdCompartment  10.342  0.044  10.386
computeThresholdNeighborhood  9.376  0.096   9.473
svmExternalData               8.514  0.036   8.549
svmClassification             8.004  0.088   8.091
candidateRelocatedProteins    6.551  0.076   6.627
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘SubCellBarCode.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/SubCellBarCode.Rcheck/00check.log’
for details.



Installation output

SubCellBarCode.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL SubCellBarCode
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-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
applyThresholdCompartment13.394 0.29213.686
applyThresholdNeighborhood10.995 0.11211.107
calRowMean0.0050.0000.005
calculateCoveredProtein0.1410.0000.140
candidateRelocatedProteins6.5510.0766.627
compareCls0.0080.0040.012
computeThresholdCompartment10.342 0.04410.386
computeThresholdNeighborhood9.3760.0969.473
convert2symbol0.0010.0000.001
hcc827Ctrl0.0030.0000.003
hcc827CtrlPSMCount0.0060.0000.007
hcc827GEF0.0020.0000.002
hcc827GEFClass0.0010.0000.001
hcc827GefPSMCount000
hcc827exon0.0000.0020.002
loadData0.0000.0010.001
markerQualityControl0.4130.0040.418
mergeCls0.0040.0000.004
mergeProbability0.0030.0000.003
plotBarcode0.5080.0000.508
plotMultipleProtein0.270.000.27
replacePrediction0.0030.0000.003
sankeyPlot0.0230.0000.022
sumProbability0.0030.0000.003
svmClassification8.0040.0888.091
svmExternalData8.5140.0368.549
tsneVisualization0.1790.0120.192