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BioC 3.5: CHECK report for GenomicDataCommons on tokay2

This page was generated on 2017-10-18 14:27:06 -0400 (Wed, 18 Oct 2017).

Package 538/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicDataCommons 1.0.5
Davis Sean
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/GenomicDataCommons
Branch: RELEASE_3_5
Last Commit: df2a841
Last Changed Date: 2017-09-14 11:59:34 -0400 (Thu, 14 Sep 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GenomicDataCommons
Version: 1.0.5
Command: rm -rf GenomicDataCommons.buildbin-libdir GenomicDataCommons.Rcheck && mkdir GenomicDataCommons.buildbin-libdir GenomicDataCommons.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomicDataCommons.buildbin-libdir GenomicDataCommons_1.0.5.tar.gz >GenomicDataCommons.Rcheck\00install.out 2>&1 && cp GenomicDataCommons.Rcheck\00install.out GenomicDataCommons-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=GenomicDataCommons.buildbin-libdir --install="check:GenomicDataCommons-install.out" --force-multiarch --no-vignettes --timings GenomicDataCommons_1.0.5.tar.gz
StartedAt: 2017-10-18 00:04:49 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 00:07:33 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 163.8 seconds
RetCode: 0
Status:  OK  
CheckDir: GenomicDataCommons.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GenomicDataCommons.buildbin-libdir GenomicDataCommons.Rcheck && mkdir GenomicDataCommons.buildbin-libdir GenomicDataCommons.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GenomicDataCommons.buildbin-libdir GenomicDataCommons_1.0.5.tar.gz >GenomicDataCommons.Rcheck\00install.out 2>&1 && cp GenomicDataCommons.Rcheck\00install.out GenomicDataCommons-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=GenomicDataCommons.buildbin-libdir --install="check:GenomicDataCommons-install.out" --force-multiarch --no-vignettes --timings GenomicDataCommons_1.0.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/GenomicDataCommons.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 'GenomicDataCommons/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GenomicDataCommons' version '1.0.5'
* 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 'GenomicDataCommons' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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
default_fields.character: no visible binding for global variable
  'defaults'
Undefined global functions or variables:
  defaults
* 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 ... NOTE
S3 methods shown with full name in documentation object 'as.data.frame.GDCResults':
  'as.data.frame.GDCResults'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... 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.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/GenomicDataCommons.Rcheck/00check.log'
for details.


GenomicDataCommons.Rcheck/00install.out:


install for i386

* installing *source* package 'GenomicDataCommons' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'GenomicDataCommons' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GenomicDataCommons' as GenomicDataCommons_1.0.5.zip
* DONE (GenomicDataCommons)

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

nameusersystemelapsed
aggregations0.500.000.75
as.data.frame.GDCResults0.360.031.92
available_expand0.030.020.08
available_fields0.050.000.14
available_values0.060.000.18
constants000
count0.110.000.29
default_fields0.050.000.17
entity_name0.090.000.15
expand0.110.000.30
faceting0.060.000.17
filtering0.240.000.47
gdc_client000
gdc_token000
gdcdata0.030.000.53
grep_fields0.060.000.10
id_field0.090.000.14
ids0.390.011.14
manifest0.220.020.39
mapping0.020.000.05
query0.140.000.23
rbindlist2000
readDNAcopy0.370.000.50
readHTSeqFile0.280.000.29
response0.080.000.25
results0.100.000.26
results_all0.090.000.27
select0.110.000.36
slicing000
status0.020.000.04
transfer000
write_manifest0.100.010.29

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

nameusersystemelapsed
aggregations0.610.010.86
as.data.frame.GDCResults0.450.000.85
available_expand0.010.000.06
available_fields0.010.020.12
available_values0.080.000.21
constants000
count0.130.010.34
default_fields0.050.000.15
entity_name0.090.000.17
expand0.130.000.33
faceting0.060.020.19
filtering0.230.000.48
gdc_client000
gdc_token000
gdcdata0.030.000.76
grep_fields0.040.000.09
id_field0.070.000.11
ids0.420.001.05
manifest0.250.030.42
mapping0.030.000.07
query0.190.000.26
rbindlist2000
readDNAcopy0.540.030.64
readHTSeqFile0.360.000.36
response0.080.000.25
results0.110.000.28
results_all0.100.000.27
select0.090.000.32
slicing000
status0.020.000.05
transfer000
write_manifest0.120.000.26