Package: goTools

Version: 1.56.0

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:goTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings goTools_1.56.0.tar.gz

StartedAt: 2019-04-13 02:49:03 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 02:51:29 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 146.4 seconds

RetCode: 0

Status:  OK

CheckDir: goTools.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:goTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings goTools_1.56.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/goTools.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 'goTools/DESCRIPTION' ... OK
* this is package 'goTools' version '1.56.0'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'goTools' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'GO.db'
A package should be listed in only one of these fields.
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... NOTE
EndNodeList: warning in get("GO:0003674", env = GOMFCHILDREN): partial
  argument match of 'env' to 'envir'
EndNodeList: warning in get("GO:0005575", env = GOCCCHILDREN): partial
  argument match of 'env' to 'envir'
EndNodeList: warning in get("GO:0008150", env = GOBPCHILDREN): partial
  argument match of 'env' to 'envir'
getGOID: warning in mget(x, env = GOenv): partial argument match of
  'env' to 'envir'
goChildren: warning in get(id, env = envi): partial argument match of
  'env' to 'envir'
goParents: warning in get(paste("GO", cat, "PARENTS", sep = ""), env =
  as.environment("package:GO.db")): partial argument match of 'env' to
  'envir'
goParents: warning in get(goid, env = envi): partial argument match of
  'env' to 'envir'
* 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
** 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/goTools.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/goTools_1.56.0.tar.gz && rm -rf goTools.buildbin-libdir && mkdir goTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=goTools.buildbin-libdir goTools_1.56.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL goTools_1.56.0.zip && rm goTools_1.56.0.tar.gz goTools_1.56.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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100 16064  100 16064    0     0   373k      0 --:--:-- --:--:-- --:--:--  412k

install for i386

* installing *source* package 'goTools' ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'goTools'
    finding HTML links ... done
    EndNodeList                             html  
    goTools-internal                        html  
    ontoCompare                             html  
    probeID                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'goTools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'goTools' as goTools_1.56.0.zip
* DONE (goTools)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'goTools' successfully unpacked and MD5 sums checked
In R CMD INSTALL