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CHECK report for CellMapper on tokay1

This page was generated on 2020-12-01 11:58:08 -0500 (Tue, 01 Dec 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE CellMapper PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 254/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CellMapper 1.16.0
Brad Nelms
Snapshot Date: 2020-11-30 14:42:56 -0500 (Mon, 30 Nov 2020)
URL: https://git.bioconductor.org/packages/CellMapper
Branch: RELEASE_3_12
Last Commit: c73a675
Last Changed Date: 2020-10-27 11:16:49 -0500 (Tue, 27 Oct 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  WARNINGS 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: CellMapper
Version: 1.16.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CellMapper.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings CellMapper_1.16.0.tar.gz
StartedAt: 2020-12-01 01:14:34 -0500 (Tue, 01 Dec 2020)
EndedAt: 2020-12-01 01:22:52 -0500 (Tue, 01 Dec 2020)
EllapsedTime: 498.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: CellMapper.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CellMapper.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings CellMapper_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/CellMapper.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CellMapper/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CellMapper' version '1.16.0'
* 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 whether package 'CellMapper' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp65PXOM/R.INSTALLee425b2449d/CellMapper/man/CMprep.Rd:51: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp65PXOM/R.INSTALLee425b2449d/CellMapper/man/CMprep.Rd:52: file link 'CellMapperData' in package 'CellMapperData' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp65PXOM/R.INSTALLee425b2449d/CellMapper/man/CMsearch.Rd:74: file link 'CellMapperData' in package 'CellMapperData' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp65PXOM/R.INSTALLee425b2449d/CellMapper/man/ExampleGeneLists.Rd:51: file link 'CellMapperData' in package 'CellMapperData' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp65PXOM/R.INSTALLee425b2449d/CellMapper/man/ExampleGeneLists.Rd:52: file link 'ExperimentHub' in package 'ExperimentHub' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp65PXOM/R.INSTALLee425b2449d/CellMapper/man/ReplicateManuscript.Rd:33: file link 'CellMapperData' in package 'CellMapperData' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp65PXOM/R.INSTALLee425b2449d/CellMapper/man/ReplicateManuscript.Rd:34: file link 'ExperimentHub' in package 'ExperimentHub' does not exist and so has been treated as a topic
  Warning: replacing previous import 'stats::sd' by 'S4Vectors::sd' when loading 'CellMapper'
  Warning: replacing previous import 'stats::var' by 'S4Vectors::var' when loading 'CellMapper'
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/CellMapper.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
ReplicateManuscript 157.6  13.46  211.86
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
ReplicateManuscript 205.7  12.87  221.33
* 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 WARNING
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/CellMapper.Rcheck/00check.log'
for details.



Installation output

CellMapper.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/CellMapper_1.16.0.tar.gz && rm -rf CellMapper.buildbin-libdir && mkdir CellMapper.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CellMapper.buildbin-libdir CellMapper_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL CellMapper_1.16.0.zip && rm CellMapper_1.16.0.tar.gz CellMapper_1.16.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 20179  100 20179    0     0  86588      0 --:--:-- --:--:-- --:--:-- 88117

install for i386

* installing *source* package 'CellMapper' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'stats::sd' by 'S4Vectors::sd' when loading 'CellMapper'
Warning: replacing previous import 'stats::var' by 'S4Vectors::var' when loading 'CellMapper'
** help
*** installing help indices
  converting help for package 'CellMapper'
    finding HTML links ... done
    CMprep                                  html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp65PXOM/R.INSTALLee425b2449d/CellMapper/man/CMprep.Rd:51: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp65PXOM/R.INSTALLee425b2449d/CellMapper/man/CMprep.Rd:52: file link 'CellMapperData' in package 'CellMapperData' does not exist and so has been treated as a topic
    CMsearch                                html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp65PXOM/R.INSTALLee425b2449d/CellMapper/man/CMsearch.Rd:74: file link 'CellMapperData' in package 'CellMapperData' does not exist and so has been treated as a topic
    CellMapperList-class                    html  
    ExampleGeneLists                        html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp65PXOM/R.INSTALLee425b2449d/CellMapper/man/ExampleGeneLists.Rd:51: file link 'CellMapperData' in package 'CellMapperData' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp65PXOM/R.INSTALLee425b2449d/CellMapper/man/ExampleGeneLists.Rd:52: file link 'ExperimentHub' in package 'ExperimentHub' does not exist and so has been treated as a topic
    ReplicateManuscript                     html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp65PXOM/R.INSTALLee425b2449d/CellMapper/man/ReplicateManuscript.Rd:33: file link 'CellMapperData' in package 'CellMapperData' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmp65PXOM/R.INSTALLee425b2449d/CellMapper/man/ReplicateManuscript.Rd:34: file link 'ExperimentHub' in package 'ExperimentHub' does not exist and so has been treated as a topic
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'stats::sd' by 'S4Vectors::sd' when loading 'CellMapper'
Warning: replacing previous import 'stats::var' by 'S4Vectors::var' when loading 'CellMapper'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'stats::sd' by 'S4Vectors::sd' when loading 'CellMapper'
Warning: replacing previous import 'stats::var' by 'S4Vectors::var' when loading 'CellMapper'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'CellMapper' ...
** testing if installed package can be loaded
Warning: replacing previous import 'stats::sd' by 'S4Vectors::sd' when loading 'CellMapper'
Warning: replacing previous import 'stats::var' by 'S4Vectors::var' when loading 'CellMapper'
* MD5 sums
packaged installation of 'CellMapper' as CellMapper_1.16.0.zip
* DONE (CellMapper)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'CellMapper' successfully unpacked and MD5 sums checked

Tests output


Example timings

CellMapper.Rcheck/examples_i386/CellMapper-Ex.timings

nameusersystemelapsed
CMprep0.160.030.19
CMsearch0.170.000.17
CellMapperList-class0.120.030.16
ExampleGeneLists0.000.040.03
ReplicateManuscript157.60 13.46211.86

CellMapper.Rcheck/examples_x64/CellMapper-Ex.timings

nameusersystemelapsed
CMprep0.190.000.18
CMsearch0.140.000.15
CellMapperList-class0.070.000.08
ExampleGeneLists0.020.000.02
ReplicateManuscript205.70 12.87221.33