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CHECK report for CellMapper on tokay1

This page was generated on 2019-04-13 11:26:58 -0400 (Sat, 13 Apr 2019).

Package 218/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CellMapper 1.8.0
Brad Nelms
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/CellMapper
Branch: RELEASE_3_8
Last Commit: d6f4e23
Last Changed Date: 2018-10-30 11:42:02 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: CellMapper
Version: 1.8.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CellMapper.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings CellMapper_1.8.0.tar.gz
StartedAt: 2019-04-13 01:04:08 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 01:11:02 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 414.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: CellMapper.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CellMapper.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings CellMapper_1.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/CellMapper.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.8.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* 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-3.8-bioc/tmpdir/RtmpAbwMc9/R.INSTALL12804f0c4ff9/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-3.8-bioc/tmpdir/RtmpAbwMc9/R.INSTALL12804f0c4ff9/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-3.8-bioc/tmpdir/RtmpAbwMc9/R.INSTALL12804f0c4ff9/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-3.8-bioc/tmpdir/RtmpAbwMc9/R.INSTALL12804f0c4ff9/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-3.8-bioc/tmpdir/RtmpAbwMc9/R.INSTALL12804f0c4ff9/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-3.8-bioc/tmpdir/RtmpAbwMc9/R.INSTALL12804f0c4ff9/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-3.8-bioc/tmpdir/RtmpAbwMc9/R.INSTALL12804f0c4ff9/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::var' by 'S4Vectors::var' when loading 'CellMapper'
  Warning: replacing previous import 'stats::sd' by 'S4Vectors::sd' when loading 'CellMapper'
See 'C:/Users/biocbuild/bbs-3.8-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 or elapsed time > 5s
                     user system elapsed
ReplicateManuscript 134.3   12.9  149.57
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
ReplicateManuscript 141.28  12.22  153.83
* 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, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.8-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/3.8/bioc/src/contrib/CellMapper_1.8.0.tar.gz && rm -rf CellMapper.buildbin-libdir && mkdir CellMapper.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CellMapper.buildbin-libdir CellMapper_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL CellMapper_1.8.0.zip && rm CellMapper_1.8.0.tar.gz CellMapper_1.8.0.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
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 20210  100 20210    0     0   525k      0 --:--:-- --:--:-- --:--:--  563k

install for i386

* installing *source* package 'CellMapper' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'stats::var' by 'S4Vectors::var' when loading 'CellMapper'
Warning: replacing previous import 'stats::sd' by 'S4Vectors::sd' when loading 'CellMapper'
** help
*** installing help indices
  converting help for package 'CellMapper'
    finding HTML links ... done
    CMprep                                  html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpAbwMc9/R.INSTALL12804f0c4ff9/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-3.8-bioc/tmpdir/RtmpAbwMc9/R.INSTALL12804f0c4ff9/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-3.8-bioc/tmpdir/RtmpAbwMc9/R.INSTALL12804f0c4ff9/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-3.8-bioc/tmpdir/RtmpAbwMc9/R.INSTALL12804f0c4ff9/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-3.8-bioc/tmpdir/RtmpAbwMc9/R.INSTALL12804f0c4ff9/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-3.8-bioc/tmpdir/RtmpAbwMc9/R.INSTALL12804f0c4ff9/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-3.8-bioc/tmpdir/RtmpAbwMc9/R.INSTALL12804f0c4ff9/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
Warning: replacing previous import 'stats::var' by 'S4Vectors::var' when loading 'CellMapper'
Warning: replacing previous import 'stats::sd' by 'S4Vectors::sd' when loading 'CellMapper'
In R CMD INSTALL

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_1.8.0.zip
* DONE (CellMapper)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'CellMapper' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

CellMapper.Rcheck/examples_i386/CellMapper-Ex.timings

nameusersystemelapsed
CMprep0.140.000.14
CMsearch0.130.000.12
CellMapperList-class0.130.000.12
ExampleGeneLists0.010.000.02
ReplicateManuscript134.30 12.90149.57

CellMapper.Rcheck/examples_x64/CellMapper-Ex.timings

nameusersystemelapsed
CMprep0.140.000.14
CMsearch0.140.020.16
CellMapperList-class0.160.000.15
ExampleGeneLists0.010.000.02
ReplicateManuscript141.28 12.22153.83