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CHECK report for ReadqPCR on tokay1

This page was generated on 2021-05-06 12:33:09 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the ReadqPCR package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1483/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ReadqPCR 1.36.0  (landing page)
James Perkins
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/ReadqPCR
Branch: RELEASE_3_12
Last Commit: 22361ee
Last Changed Date: 2020-10-27 10:42:02 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: ReadqPCR
Version: 1.36.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ReadqPCR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ReadqPCR_1.36.0.tar.gz
StartedAt: 2021-05-06 06:03:14 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 06:04:00 -0400 (Thu, 06 May 2021)
EllapsedTime: 46.0 seconds
RetCode: 0
Status:   WARNINGS   
CheckDir: ReadqPCR.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:ReadqPCR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ReadqPCR_1.36.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/ReadqPCR.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ReadqPCR/DESCRIPTION' ... OK
* this is package 'ReadqPCR' version '1.36.0'
* 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 'ReadqPCR' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpQ7YePK/R.INSTALL9ac7bcd5519/ReadqPCR/man/qpcR2CyclesSet.Rd:30: file link 'reps' in package 'qpcR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpQ7YePK/R.INSTALL9ac7bcd5519/ReadqPCR/man/readLC480.Rd:61: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpQ7YePK/R.INSTALL9ac7bcd5519/ReadqPCR/man/readLC480SampleInfo.Rd:54: file link 'AnnotatedDataFrame-class' in package 'Biobase' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/ReadqPCR.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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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/ReadqPCR.Rcheck/00check.log'
for details.



Installation output

ReadqPCR.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/ReadqPCR_1.36.0.tar.gz && rm -rf ReadqPCR.buildbin-libdir && mkdir ReadqPCR.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ReadqPCR.buildbin-libdir ReadqPCR_1.36.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL ReadqPCR_1.36.0.zip && rm ReadqPCR_1.36.0.tar.gz ReadqPCR_1.36.0.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  431k  100  431k    0     0  22.5M      0 --:--:-- --:--:-- --:--:-- 23.4M

install for i386

* installing *source* package 'ReadqPCR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ReadqPCR'
    finding HTML links ... done
    CyclesSet-class                         html  
    ReadqPCR-package                        html  
    merge                                   html  
    qPCRBatch-class                         html  
    qpcR2CyclesSet                          html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpQ7YePK/R.INSTALL9ac7bcd5519/ReadqPCR/man/qpcR2CyclesSet.Rd:30: file link 'reps' in package 'qpcR' does not exist and so has been treated as a topic
    read.qPCR                               html  
    read.taqman                             html  
    readLC480                               html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpQ7YePK/R.INSTALL9ac7bcd5519/ReadqPCR/man/readLC480.Rd:61: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
    readLC480SampleInfo                     html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpQ7YePK/R.INSTALL9ac7bcd5519/ReadqPCR/man/readLC480SampleInfo.Rd:54: file link 'AnnotatedDataFrame-class' in package 'Biobase' does not exist and so has been treated as a topic
** building package indices
** installing vignettes
   'ReadqPCR.Rnw' 
** 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

install for x64

* installing *source* package 'ReadqPCR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ReadqPCR' as ReadqPCR_1.36.0.zip
* DONE (ReadqPCR)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'ReadqPCR' successfully unpacked and MD5 sums checked

Tests output


Example timings

ReadqPCR.Rcheck/examples_i386/ReadqPCR-Ex.timings

nameusersystemelapsed
ReadqPCR-package000
merge0.110.000.10
qpcR2CyclesSet1.580.211.79
read.qPCR0.060.000.06
read.taqman0.240.000.26
readLC4800.140.000.14
readLC480SampleInfo000

ReadqPCR.Rcheck/examples_x64/ReadqPCR-Ex.timings

nameusersystemelapsed
ReadqPCR-package000
merge0.090.020.10
qpcR2CyclesSet1.500.121.63
read.qPCR0.060.000.06
read.taqman0.20.00.2
readLC4800.100.000.09
readLC480SampleInfo000