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BioC 3.5: CHECK report for coMET on tokay2

This page was generated on 2017-10-18 14:24:20 -0400 (Wed, 18 Oct 2017).

Package 263/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
coMET 1.8.0
Tiphaine Martin
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/coMET
Branch: RELEASE_3_5
Last Commit: 04f4c5f
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: coMET
Version: 1.8.0
Command: rm -rf coMET.buildbin-libdir coMET.Rcheck && mkdir coMET.buildbin-libdir coMET.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=coMET.buildbin-libdir coMET_1.8.0.tar.gz >coMET.Rcheck\00install.out 2>&1 && cp coMET.Rcheck\00install.out coMET-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=coMET.buildbin-libdir --install="check:coMET-install.out" --force-multiarch --no-vignettes --timings coMET_1.8.0.tar.gz
StartedAt: 2017-10-17 22:56:02 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 23:20:14 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 1452.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: coMET.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf coMET.buildbin-libdir coMET.Rcheck && mkdir coMET.buildbin-libdir coMET.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=coMET.buildbin-libdir coMET_1.8.0.tar.gz >coMET.Rcheck\00install.out 2>&1 && cp coMET.Rcheck\00install.out coMET-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=coMET.buildbin-libdir --install="check:coMET-install.out" --force-multiarch --no-vignettes --timings coMET_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/coMET.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 'coMET/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'coMET' version '1.8.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'grid' 'biomaRt' 'Gviz' 'psych' 'ggbio' 'trackViewer'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ... WARNING
Found the following significant warnings:
  WARNING: omitting pointless dependence on 'R' without a version requirement
See 'C:/Users/biocbuild/bbs-3.5-bioc/meat/coMET.Rcheck/00install.out' for details.
* 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'
geneExpression_GTEx: no visible global function definition for 'as'
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:
  as 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
Consider adding
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... WARNING
  Error in if (dep$op != ">=") next : argument is of length zero
  Calls: <Anonymous>
  Execution halted
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
comet.web     18.05   0.72  383.81
coMET-package  7.27   0.45   32.18
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
comet.web     18.55   0.63  391.73
coMET-package  8.22   0.40   34.62
comet          4.80   0.08    5.36
* 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: 2 WARNINGs, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/coMET.Rcheck/00check.log'
for details.


coMET.Rcheck/00install.out:


install for i386

WARNING: omitting pointless dependence on 'R' without a version requirement
* installing *source* package 'coMET' ...
** 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

WARNING: omitting pointless dependence on 'R' without a version requirement
* installing *source* package 'coMET' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'coMET' as coMET_1.8.0.zip
* DONE (coMET)

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

nameusersystemelapsed
COSMIC_UCSC2.380.062.44
ChIPTF_ENCODE0.450.050.50
ClinVarCnv_UCSC0.80.00.8
ClinVarMain_UCSC0.340.000.34
CoreillCNV_UCSC0.290.000.28
DNAse_UCSC1.110.001.11
DNaseI_FANTOM0.640.000.64
DNaseI_RoadMap0.410.000.40
GAD_UCSC0.280.000.28
GWAScatalog_UCSC0.260.000.27
GeneReviews_UCSC0.550.000.55
HiCdata2matrix0.030.010.04
HistoneAll_UCSC3.000.023.01
HistoneOne_UCSC0.330.010.35
ISCA_UCSC000
TFBS_FANTOM0.280.000.28
bindingMotifsBiomart_ENSEMBL0.220.030.25
chrUCSC2ENSEMBL000
chromHMM_RoadMap0.810.020.83
chromatinHMMAll_UCSC3.670.033.70
chromatinHMMOne_UCSC0.630.020.64
coMET-package 7.27 0.4532.18
comet3.400.063.47
comet.list0.720.000.72
comet.web 18.05 0.72383.81
cpgIslands_UCSC0.140.000.15
dgfootprints_RoadMap0.690.060.75
eQTL101
eQTL_GTEx0.980.000.98
gcContent_UCSC0.360.020.37
genesName_ENSEMBL0.000.020.02
genes_ENSEMBL0.630.010.64
imprintedGenes_GTEx3.110.033.56
interestGenes_ENSEMBL0.450.020.47
interestTranscript_ENSEMBL0.640.010.66
knownGenes_UCSC0.810.000.81
metQTL0.740.000.74
miRNATargetRegionsBiomart_ENSEMBL0.070.000.07
otherRegulatoryRegionsBiomart_ENSEMBL0.130.000.13
psiQTL_GTEx0.780.020.80
refGenes_UCSC0.700.010.71
regulationBiomart_ENSEMBL0.240.000.24
regulatoryEvidenceBiomart_ENSEMBL0.20.00.2
regulatoryFeaturesBiomart_ENSEMBL0.170.020.18
regulatorySegmentsBiomart_ENSEMBL0.190.050.24
repeatMasker_UCSC0.430.000.44
segmentalDups_UCSC0.300.000.29
snpBiomart_ENSEMBL0.330.000.33
snpLocations_UCSC0.800.010.81
structureBiomart_ENSEMBL0.390.020.41
transcript_ENSEMBL1.460.011.48
xenorefGenes_UCSC0.430.020.44

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

nameusersystemelapsed
COSMIC_UCSC2.640.042.67
ChIPTF_ENCODE0.630.010.64
ClinVarCnv_UCSC0.960.020.97
ClinVarMain_UCSC0.390.010.40
CoreillCNV_UCSC0.330.020.35
DNAse_UCSC0.430.010.45
DNaseI_FANTOM0.710.000.70
DNaseI_RoadMap0.320.000.33
GAD_UCSC0.360.020.38
GWAScatalog_UCSC0.270.000.26
GeneReviews_UCSC0.590.000.59
HiCdata2matrix0.050.000.05
HistoneAll_UCSC3.360.003.36
HistoneOne_UCSC0.340.000.34
ISCA_UCSC0.020.000.02
TFBS_FANTOM0.280.000.28
bindingMotifsBiomart_ENSEMBL0.200.020.22
chrUCSC2ENSEMBL000
chromHMM_RoadMap0.820.000.81
chromatinHMMAll_UCSC3.690.013.70
chromatinHMMOne_UCSC0.670.020.69
coMET-package 8.22 0.4034.62
comet4.800.085.36
comet.list1.400.001.41
comet.web 18.55 0.63391.73
cpgIslands_UCSC0.250.000.25
dgfootprints_RoadMap0.720.010.74
eQTL1.060.021.08
eQTL_GTEx1.160.001.15
gcContent_UCSC0.510.000.52
genesName_ENSEMBL0.020.000.01
genes_ENSEMBL0.800.010.82
imprintedGenes_GTEx3.810.054.22
interestGenes_ENSEMBL0.530.000.53
interestTranscript_ENSEMBL0.720.020.73
knownGenes_UCSC0.860.000.86
metQTL0.890.010.91
miRNATargetRegionsBiomart_ENSEMBL0.040.020.06
otherRegulatoryRegionsBiomart_ENSEMBL0.130.010.15
psiQTL_GTEx0.810.020.82
refGenes_UCSC0.730.010.75
regulationBiomart_ENSEMBL0.250.000.25
regulatoryEvidenceBiomart_ENSEMBL0.370.020.39
regulatoryFeaturesBiomart_ENSEMBL0.270.010.28
regulatorySegmentsBiomart_ENSEMBL0.330.040.36
repeatMasker_UCSC0.70.00.7
segmentalDups_UCSC0.340.010.36
snpBiomart_ENSEMBL0.390.000.39
snpLocations_UCSC0.890.020.91
structureBiomart_ENSEMBL0.350.010.36
transcript_ENSEMBL1.590.021.61
xenorefGenes_UCSC0.490.000.48