Package: ReadqPCR

Version: 1.29.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ReadqPCR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ReadqPCR_1.29.0.tar.gz

StartedAt: 2019-04-09 05:18:37 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 05:19:27 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 50.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: ReadqPCR.Rcheck

Warnings: 1

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ReadqPCR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ReadqPCR_1.29.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/ReadqPCR.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* 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 '1.29.0'
* 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-3.9-bioc/tmpdir/Rtmpoxtkgq/R.INSTALL5bc5d144b66/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-3.9-bioc/tmpdir/Rtmpoxtkgq/R.INSTALL5bc5d144b66/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-3.9-bioc/tmpdir/Rtmpoxtkgq/R.INSTALL5bc5d144b66/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-3.9-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-3.9-bioc/meat/ReadqPCR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/ReadqPCR_1.29.0.tar.gz && rm -rf ReadqPCR.buildbin-libdir && mkdir ReadqPCR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ReadqPCR.buildbin-libdir ReadqPCR_1.29.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL ReadqPCR_1.29.0.zip && rm ReadqPCR_1.29.0.tar.gz ReadqPCR_1.29.0.zip
###
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install for i386

* installing *source* package 'ReadqPCR' ...
** 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-3.9-bioc/tmpdir/Rtmpoxtkgq/R.INSTALL5bc5d144b66/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-3.9-bioc/tmpdir/Rtmpoxtkgq/R.INSTALL5bc5d144b66/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-3.9-bioc/tmpdir/Rtmpoxtkgq/R.INSTALL5bc5d144b66/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_1.29.0.zip
* DONE (ReadqPCR)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'ReadqPCR' successfully unpacked and MD5 sums checked