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CHECK report for FoldGO on tokay1

This page was generated on 2019-04-13 11:29:41 -0400 (Sat, 13 Apr 2019).

Package 557/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FoldGO 1.0.2
Daniil Wiebe
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/FoldGO
Branch: RELEASE_3_8
Last Commit: bed1e14
Last Changed Date: 2019-04-12 06:02:55 -0400 (Fri, 12 Apr 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK YES, new version is higher than in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK YES, new version is higher than in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK YES, new version is higher than in internal repository

Summary

Package: FoldGO
Version: 1.0.2
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FoldGO.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings FoldGO_1.0.2.tar.gz
StartedAt: 2019-04-13 02:20:18 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 02:23:38 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 200.9 seconds
RetCode: 0
Status:  OK  
CheckDir: FoldGO.Rcheck
Warnings: 0

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:FoldGO.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings FoldGO_1.0.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/FoldGO.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 'FoldGO/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'FoldGO' version '1.0.2'
* package encoding: UTF-8
* 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 'FoldGO' can be installed ... OK
* 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
plot-FoldSpecTest-ANY-method  5.3      0     5.3
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
plot-FoldSpecTest-ANY-method 5.53      0    5.53
* 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: OK


Installation output

FoldGO.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/FoldGO_1.0.2.tar.gz && rm -rf FoldGO.buildbin-libdir && mkdir FoldGO.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=FoldGO.buildbin-libdir FoldGO_1.0.2.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL FoldGO_1.0.2.zip && rm FoldGO_1.0.2.tar.gz FoldGO_1.0.2.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 1747k  100 1747k    0     0  31.9M      0 --:--:-- --:--:-- --:--:-- 34.8M

install for i386

* installing *source* package 'FoldGO' ...
** R
** data
*** moving datasets to lazyload DB

** inst
** byte-compile and prepare package for lazy loading
in method for 'getAnnotation' with signature '"MgsaSets"': no definition for class "MgsaSets"
** help
*** installing help indices
  converting help for package 'FoldGO'
    finding HTML links ... done
    examdata_bg                             html  
    examdata_degs                           html  
    examdata_objs                           html  
    fagroupstopgo_class                     html  
    foldspectest_class                      html  
    gafreader_class                         html  
    genegroups_class                        html  
    getAnnotation                           html  
    getWholeIntName                         html  
    plot-FoldSpecTest-ANY-method            html  
    rna_seq_data                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'FoldGO' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'FoldGO' as FoldGO_1.0.2.zip
* DONE (FoldGO)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'FoldGO' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

FoldGO.Rcheck/examples_i386/FoldGO-Ex.timings

nameusersystemelapsed
examdata_bg0.020.000.01
examdata_degs000
examdata_objs000
fagroupstopgo_class4.240.154.59
foldspectest_class2.950.002.96
gafreader_class2.420.242.65
genegroups_class0.020.010.03
getAnnotation000
getWholeIntName2.390.022.41
plot-FoldSpecTest-ANY-method5.30.05.3

FoldGO.Rcheck/examples_x64/FoldGO-Ex.timings

nameusersystemelapsed
examdata_bg0.000.010.02
examdata_degs000
examdata_objs0.000.020.02
fagroupstopgo_class4.680.084.75
foldspectest_class3.150.003.16
gafreader_class2.330.202.53
genegroups_class0.020.010.03
getAnnotation000
getWholeIntName2.420.002.42
plot-FoldSpecTest-ANY-method5.530.005.53