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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IVAS.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings IVAS_2.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/IVAS.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 'IVAS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'IVAS' version '2.10.0'
* 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 'IVAS' can be installed ... WARNING
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpwrTz6J/R.INSTALL2ba05d692100/IVAS/man/RatioFromFPKM.Rd:46: file link 'isActiveSeq' in package 'GenomicFeatures' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpwrTz6J/R.INSTALL2ba05d692100/IVAS/man/Splicingfinder.Rd:41: file link 'isActiveSeq' in package 'GenomicFeatures' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpwrTz6J/R.INSTALL2ba05d692100/IVAS/man/chrseparate.Rd:31: file link 'isActiveSeq' in package 'GenomicFeatures' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpwrTz6J/R.INSTALL2ba05d692100/IVAS/man/findAlternative.Rd:44: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpwrTz6J/R.INSTALL2ba05d692100/IVAS/man/findAlternative.Rd:45: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpwrTz6J/R.INSTALL2ba05d692100/IVAS/man/findOversnp.Rd:29: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/IVAS.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
* 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
saveBplot   10.91   0.10   11.01
ASdb-class  10.37   0.12   10.50
sQTLsFinder 10.08   0.15   10.23
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
saveBplot     16.00   0.06   16.34
ASdb-class    15.47   0.11   15.59
sQTLsFinder   12.31   0.08   12.39
RatioFromFPKM  7.45   0.02    7.49
* 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/IVAS.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/IVAS_2.10.0.tar.gz && rm -rf IVAS.buildbin-libdir && mkdir IVAS.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=IVAS.buildbin-libdir IVAS_2.10.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL IVAS_2.10.0.zip && rm IVAS_2.10.0.tar.gz IVAS_2.10.0.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 75197  100 75197    0     0  4697k      0 --:--:-- --:--:-- --:--:-- 4895k

install for i386

* installing *source* package 'IVAS' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Note: next used in wrong context: no loop is visible 
** help
*** installing help indices
  converting help for package 'IVAS'
    finding HTML links ... done
    ASdb-class                              html  
    CalSigSNP                               html  
    IVAS-deprecated                         html  
    IVAS-package                            html  
    MsqtlFinder                             html  
    RatioFromFPKM                           html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpwrTz6J/R.INSTALL2ba05d692100/IVAS/man/RatioFromFPKM.Rd:46: file link 'isActiveSeq' in package 'GenomicFeatures' does not exist and so has been treated as a topic
    Splicingfinder                          html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpwrTz6J/R.INSTALL2ba05d692100/IVAS/man/Splicingfinder.Rd:41: file link 'isActiveSeq' in package 'GenomicFeatures' does not exist and so has been treated as a topic
    calSignificant                          html  
    chrseparate                             html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpwrTz6J/R.INSTALL2ba05d692100/IVAS/man/chrseparate.Rd:31: file link 'isActiveSeq' in package 'GenomicFeatures' does not exist and so has been treated as a topic
    findAlternative                         html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpwrTz6J/R.INSTALL2ba05d692100/IVAS/man/findAlternative.Rd:44: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpwrTz6J/R.INSTALL2ba05d692100/IVAS/man/findAlternative.Rd:45: file link 'IRanges' in package 'IRanges' does not exist and so has been treated as a topic
    findOversnp                             html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpwrTz6J/R.INSTALL2ba05d692100/IVAS/man/findOversnp.Rd:29: file link 'findOverlaps' in package 'IRanges' does not exist and so has been treated as a topic
    sQTLsFinder                             html  
    sampleexp                               html  
    samplesnp                               html  
    samplesnplocus                          html  
    saveBplot                               html  
    sqtlfinder                              html  
** 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

install for x64

* installing *source* package 'IVAS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'IVAS' as IVAS_2.10.0.zip
* DONE (IVAS)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'IVAS' successfully unpacked and MD5 sums checked