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BioC 3.2: CHECK report for genomes on windows1.bioconductor.org

This page was generated on 2015-10-27 17:29:10 -0400 (Tue, 27 Oct 2015).

Package 420/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genomes 2.16.0
Chris Stubben
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/genomes
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: genomes
Version: 2.16.0
Command: rm -rf genomes.buildbin-libdir genomes.Rcheck && mkdir genomes.buildbin-libdir genomes.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=genomes.buildbin-libdir genomes_2.16.0.tar.gz >genomes.Rcheck\00install.out 2>&1 && cp genomes.Rcheck\00install.out genomes-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=genomes.buildbin-libdir --install="check:genomes-install.out" --force-multiarch --no-vignettes --timings genomes_2.16.0.tar.gz
StartedAt: 2015-10-27 02:05:34 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 02:08:16 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 162.6 seconds
RetCode: 0
Status:  OK  
CheckDir: genomes.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf genomes.buildbin-libdir genomes.Rcheck && mkdir genomes.buildbin-libdir genomes.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=genomes.buildbin-libdir genomes_2.16.0.tar.gz >genomes.Rcheck\00install.out 2>&1 && cp genomes.Rcheck\00install.out genomes-install.out  && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=genomes.buildbin-libdir --install="check:genomes-install.out" --force-multiarch --no-vignettes --timings genomes_2.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/genomes.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'genomes/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'genomes' version '2.16.0'
* 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 'genomes' 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.
* 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
read.genemark: no visible global function definition for 'isCircular<-'
read.genemark: no visible global function definition for 'seqlengths<-'
read.genemark: no visible global function definition for 'metadata<-'
read.gff: no visible global function definition for 'seqlengths<-'
read.gff: no visible global function definition for 'metadata<-'
read.glimmer: no visible global function definition for 'isCircular<-'
read.glimmer: no visible global function definition for 'seqlengths<-'
read.glimmer: no visible global function definition for 'metadata<-'
read.ncbi.ftp : <anonymous>: no visible global function definition for
  'metadata'
read.ncbi.ftp: no visible global function definition for 'seqlengths'
read.ncbi.ftp: no visible global function definition for 'seqlevels<-'
read.ncbi.ftp: no visible global function definition for 'seqlevels'
read.ncbi.ftp: no visible global function definition for 'metadata<-'
read.prodigal: no visible global function definition for 'isCircular<-'
read.prodigal: no visible global function definition for 'seqlengths<-'
read.prodigal: no visible global function definition for 'metadata<-'
read.ptt: no visible global function definition for 'isCircular<-'
read.ptt: no visible global function definition for 'seqlengths<-'
read.ptt: no visible global function definition for 'metadata<-'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [22s] OK
** running examples for arch 'x64' ... [22s] 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:/biocbld/bbs-3.2-bioc/meat/genomes.Rcheck/00check.log'
for details.


genomes.Rcheck/00install.out:


install for i386

* installing *source* package 'genomes' ...
** R
** data
** 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 'genomes' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'genomes' as genomes_2.16.0.zip
* DONE (genomes)

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

nameusersystemelapsed
doublingTime1.250.041.30
efetch000
einfo000
elink000
esearch000
esummary000
euks0.220.000.22
ftpList000
genomes-lines0.710.020.72
genomes-plot0.670.030.70
genomes-print0.440.000.44
genomes-summary0.030.020.04
genomes-update000
genomes101
genus0.50.00.5
image20.810.000.81
like0.970.010.99
ncbiGenome000
ncbiNucleotide000
ncbiProject000
ncbiPubmed000
ncbiRelease0.350.051.10
ncbiSubmit000
ncbiTaxonomy000
plotby1.060.001.07
proks1.160.021.17
read.genemark0.060.000.19
read.gff0.030.010.18
read.glimmer0.050.000.32
read.ncbi.ftp000
read.prodigal3.331.505.00
read.ptt1.160.741.97
species0.570.010.59
table20.070.000.07
virus0.120.020.14
year0.560.030.59

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

nameusersystemelapsed
doublingTime1.670.001.67
efetch000
einfo000
elink0.010.000.02
esearch000
esummary000
euks0.100.000.09
ftpList000
genomes-lines0.840.000.84
genomes-plot0.860.000.86
genomes-print0.360.010.38
genomes-summary0.060.000.06
genomes-update000
genomes0.960.000.95
genus0.420.020.44
image20.900.020.92
like0.930.000.93
ncbiGenome000
ncbiNucleotide000
ncbiProject000
ncbiPubmed000
ncbiRelease0.260.091.17
ncbiSubmit000
ncbiTaxonomy000
plotby1.390.001.39
proks1.000.021.02
read.genemark0.080.010.20
read.gff0.060.020.17
read.glimmer0.110.000.36
read.ncbi.ftp000
read.prodigal2.111.543.75
read.ptt1.040.531.62
species0.860.000.86
table20.050.000.05
virus0.140.020.15
year0.530.000.53