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BioC 3.3: CHECK report for coMET on moscato2

This page was generated on 2016-10-13 12:53:30 -0700 (Thu, 13 Oct 2016).

Package 229/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
coMET 1.4.4
Tiphaine Martin
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/coMET
Last Changed Rev: 118502 / Revision: 122332
Last Changed Date: 2016-06-12 09:31:06 -0700 (Sun, 12 Jun 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  ERROR  skipped 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  ERROR  skipped  skipped 

Summary

Package: coMET
Version: 1.4.4
Command: rm -rf coMET.buildbin-libdir coMET.Rcheck && mkdir coMET.buildbin-libdir coMET.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=coMET.buildbin-libdir coMET_1.4.4.tar.gz >coMET.Rcheck\00install.out 2>&1 && cp coMET.Rcheck\00install.out coMET-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=coMET.buildbin-libdir --install="check:coMET-install.out" --force-multiarch --no-vignettes --timings coMET_1.4.4.tar.gz
StartedAt: 2016-10-13 02:27:03 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 02:56:04 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 1741.1 seconds
RetCode: 0
Status:  OK  
CheckDir: coMET.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf coMET.buildbin-libdir coMET.Rcheck && mkdir coMET.buildbin-libdir coMET.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=coMET.buildbin-libdir coMET_1.4.4.tar.gz >coMET.Rcheck\00install.out 2>&1 && cp coMET.Rcheck\00install.out coMET-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=coMET.buildbin-libdir --install="check:coMET-install.out" --force-multiarch --no-vignettes --timings coMET_1.4.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/coMET.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'coMET/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'coMET' version '1.4.4'
* 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 'coMET' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 17.4Mb
  sub-directories of 1Mb or more:
    data      9.8Mb
    doc       2.7Mb
    extdata   4.5Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
** 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
chromHMM_RoadMap: no visible binding for global variable
  'chromosome_stop'
chromHMM_RoadMap: no visible binding for global variable
  'chromosome_start'
chromHMM_RoadMap: no visible binding for global variable
  'chromosome_name'
eQTL: no visible binding for global variable 'chromosome_stop'
eQTL: no visible binding for global variable 'chromosome_start'
eQTL: no visible binding for global variable 'chromosome_name'
eQTL_GTEx: no visible binding for global variable 'snp_pos'
eQTL_GTEx: no visible binding for global variable 'snp_chrom'
eQTL_GTEx: no visible binding for global variable 'gene_start'
eQTL_GTEx: no visible binding for global variable 'gene_stop'
eQTL_GTEx: no visible binding for global variable 'gene_chr'
metQTL: no visible binding for global variable 'chromosome_stop'
metQTL: no visible binding for global variable 'chromosome_start'
metQTL: no visible binding for global variable 'chromosome_name'
psiQTL_GTEx: no visible binding for global variable 'pos_snp'
psiQTL_GTEx: no visible binding for global variable 'chr_snp'
psiQTL_GTEx: no visible binding for global variable 'pos_middle_exon'
psiQTL_GTEx: no visible binding for global variable 'chr_exon'
Undefined global functions or variables:
  chr_exon chr_snp chromosome_name chromosome_start chromosome_stop
  gene_chr gene_start gene_stop pos_middle_exon pos_snp snp_chrom
  snp_pos
* 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' ... NOTE
The following directory looks like a leftover from 'knitr':
  'figure'
Please remove from your package.
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
comet.web           18.22   0.25  373.28
coMET-package        5.88   0.12   27.83
imprintedGenes_GTEx  4.72   0.03    5.69
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
comet.web             21.17   0.38  402.26
coMET-package          9.75   0.66   33.00
chromatinHMMAll_UCSC   6.72   0.01    6.74
HistoneAll_UCSC        5.66   0.00    5.66
imprintedGenes_GTEx    4.66   0.03    6.88
interestGenes_ENSEMBL  1.20   0.01    8.80
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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: 4 NOTEs
See
  'E:/biocbld/bbs-3.3-bioc/meat/coMET.Rcheck/00check.log'
for details.


coMET.Rcheck/00install.out:


install for i386

* installing *source* package 'coMET' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio'

install for x64

* installing *source* package 'coMET' ...
** testing if installed package can be loaded
Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio'
* MD5 sums
packaged installation of 'coMET' as coMET_1.4.4.zip
* DONE (coMET)

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

nameusersystemelapsed
COSMIC_UCSC0.900.040.93
ChIPTF_ENCODE0.120.000.12
ClinVarCnv_UCSC0.360.010.38
ClinVarMain_UCSC0.380.000.37
CoreillCNV_UCSC0.400.020.42
DNAse_UCSC0.420.000.43
DNaseI_FANTOM0.550.000.54
DNaseI_RoadMap0.50.00.5
GAD_UCSC0.560.000.56
GWAScatalog_UCSC0.500.010.52
GeneReviews_UCSC0.560.020.57
HiCdata2matrix0.030.000.04
HistoneAll_UCSC4.480.014.49
HistoneOne_UCSC0.30.00.3
ISCA_UCSC000
TFBS_FANTOM0.280.020.29
bindingMotifsBiomart_ENSEMBL0.240.020.25
chrUCSC2ENSEMBL000
chromHMM_RoadMap0.870.011.24
chromatinHMMAll_UCSC4.060.004.06
chromatinHMMOne_UCSC0.590.020.61
coMET-package 5.88 0.1227.83
comet2.950.023.13
comet.list1.800.011.81
comet.web 18.22 0.25373.28
cpgIslands_UCSC0.20.00.2
dgfootprints_RoadMap1.030.001.03
eQTL1.400.031.79
eQTL_GTEx1.580.001.57
gcContent_UCSC0.280.020.30
genesName_ENSEMBL000
genes_ENSEMBL1.030.021.04
imprintedGenes_GTEx4.720.035.69
interestGenes_ENSEMBL0.910.010.92
interestTranscript_ENSEMBL1.120.021.14
knownGenes_UCSC1.650.011.67
metQTL1.440.021.50
miRNATargetRegionsBiomart_ENSEMBL0.120.000.12
otherRegulatoryRegionsBiomart_ENSEMBL0.190.010.20
psiQTL_GTEx1.040.001.05
refGenes_UCSC1.270.021.28
regulationBiomart_ENSEMBL0.280.000.28
regulatoryEvidenceBiomart_ENSEMBL0.250.000.25
regulatoryFeaturesBiomart_ENSEMBL0.360.010.38
regulatorySegmentsBiomart_ENSEMBL0.390.000.39
repeatMasker_UCSC0.570.000.58
segmentalDups_UCSC0.440.020.45
snpBiomart_ENSEMBL0.480.000.48
snpLocations_UCSC1.30.01.3
structureBiomart_ENSEMBL0.510.000.51
transcript_ENSEMBL2.800.003.14
xenorefGenes_UCSC0.680.010.70

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

nameusersystemelapsed
COSMIC_UCSC1.130.021.14
ChIPTF_ENCODE0.170.010.18
ClinVarCnv_UCSC0.650.020.68
ClinVarMain_UCSC0.560.010.57
CoreillCNV_UCSC0.490.020.50
DNAse_UCSC0.620.000.63
DNaseI_FANTOM0.830.000.82
DNaseI_RoadMap0.640.000.64
GAD_UCSC1.170.011.20
GWAScatalog_UCSC0.540.020.56
GeneReviews_UCSC1.000.011.02
HiCdata2matrix0.050.000.05
HistoneAll_UCSC5.660.005.66
HistoneOne_UCSC0.390.020.40
ISCA_UCSC0.020.000.02
TFBS_FANTOM0.50.00.5
bindingMotifsBiomart_ENSEMBL0.370.010.39
chrUCSC2ENSEMBL000
chromHMM_RoadMap1.580.021.59
chromatinHMMAll_UCSC6.720.016.74
chromatinHMMOne_UCSC0.670.000.67
coMET-package 9.75 0.6633.00
comet3.750.043.79
comet.list1.820.001.83
comet.web 21.17 0.38402.26
cpgIslands_UCSC0.270.013.06
dgfootprints_RoadMap0.860.022.31
eQTL1.800.064.10
eQTL_GTEx2.410.023.59
gcContent_UCSC0.450.001.71
genesName_ENSEMBL0.00.00.8
genes_ENSEMBL1.230.001.35
imprintedGenes_GTEx4.660.036.88
interestGenes_ENSEMBL1.200.018.80
interestTranscript_ENSEMBL1.110.001.70
knownGenes_UCSC1.400.001.61
metQTL1.270.042.09
miRNATargetRegionsBiomart_ENSEMBL0.140.001.72
otherRegulatoryRegionsBiomart_ENSEMBL0.280.010.53
psiQTL_GTEx1.120.002.70
refGenes_UCSC1.070.021.09
regulationBiomart_ENSEMBL0.520.004.12
regulatoryEvidenceBiomart_ENSEMBL0.340.031.58
regulatoryFeaturesBiomart_ENSEMBL0.380.030.71
regulatorySegmentsBiomart_ENSEMBL0.320.031.08
repeatMasker_UCSC0.810.000.99
segmentalDups_UCSC0.560.021.84
snpBiomart_ENSEMBL0.660.012.84
snpLocations_UCSC1.650.002.11
structureBiomart_ENSEMBL0.490.000.67
transcript_ENSEMBL2.070.002.51
xenorefGenes_UCSC0.670.004.57