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BioC 3.5: CHECK report for biomformat on tokay2

This page was generated on 2017-10-18 14:25:26 -0400 (Wed, 18 Oct 2017).

Package 128/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biomformat 1.4.0
Paul J. McMurdie
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/biomformat
Branch: RELEASE_3_5
Last Commit: 83b4b18
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: biomformat
Version: 1.4.0
Command: rm -rf biomformat.buildbin-libdir biomformat.Rcheck && mkdir biomformat.buildbin-libdir biomformat.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=biomformat.buildbin-libdir biomformat_1.4.0.tar.gz >biomformat.Rcheck\00install.out 2>&1 && cp biomformat.Rcheck\00install.out biomformat-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=biomformat.buildbin-libdir --install="check:biomformat-install.out" --force-multiarch --no-vignettes --timings biomformat_1.4.0.tar.gz
StartedAt: 2017-10-17 22:20:54 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 22:22:38 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 104.3 seconds
RetCode: 0
Status:  OK  
CheckDir: biomformat.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf biomformat.buildbin-libdir biomformat.Rcheck && mkdir biomformat.buildbin-libdir biomformat.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=biomformat.buildbin-libdir biomformat_1.4.0.tar.gz >biomformat.Rcheck\00install.out 2>&1 && cp biomformat.Rcheck\00install.out biomformat-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=biomformat.buildbin-libdir --install="check:biomformat-install.out" --force-multiarch --no-vignettes --timings biomformat_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/biomformat.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'biomformat/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'biomformat' version '1.4.0'
* 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 'biomformat' 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 ... NOTE
make_biom: no visible global function definition for 'packageVersion'
namedList: no visible global function definition for 'setNames'
Undefined global functions or variables:
  packageVersion setNames
Consider adding
  importFrom("stats", "setNames")
  importFrom("utils", "packageVersion")
to your NAMESPACE file.
* 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 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat-biomformat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat-biomformat.R'
 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/biomformat.Rcheck/00check.log'
for details.


biomformat.Rcheck/00install.out:


install for i386

* installing *source* package 'biomformat' ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'nrow' from package 'base' in package 'biomformat'
Creating a generic function for 'ncol' from package 'base' in package 'biomformat'
Creating a generic function for 'rownames' from package 'base' in package 'biomformat'
Creating a generic function for 'colnames' from package 'base' in package 'biomformat'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'biomformat' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'biomformat' as biomformat_1.4.0.zip
* DONE (biomformat)

biomformat.Rcheck/examples_i386/biomformat-Ex.timings:

nameusersystemelapsed
biom-class0.270.040.31
biom-methods0.090.000.09
biom_data-methods0.120.020.14
biom_shape-methods0.020.000.02
colnames-methods000
header-methods000
make_biom0.080.000.08
matrix_element_type-methods000
ncol-methods0.020.000.01
nrow-methods000
observation_metadata-methods0.030.000.04
read_biom0.010.000.01
read_hdf5_biom0.270.001.02
rownames-methods000
sample_metadata-methods0.050.000.04
show-methods000
write_biom0.010.000.02

biomformat.Rcheck/examples_x64/biomformat-Ex.timings:

nameusersystemelapsed
biom-class0.360.000.36
biom-methods0.110.000.11
biom_data-methods0.160.000.16
biom_shape-methods0.010.000.02
colnames-methods000
header-methods000
make_biom0.110.000.10
matrix_element_type-methods000
ncol-methods000
nrow-methods0.020.000.02
observation_metadata-methods0.030.000.03
read_biom000
read_hdf5_biom0.260.021.40
rownames-methods000
sample_metadata-methods0.050.000.05
show-methods0.010.000.02
write_biom0.020.000.01