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BioC 3.2: CHECK report for coMET on moscato1

This page was generated on 2016-04-23 10:21:15 -0700 (Sat, 23 Apr 2016).

Package 212/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
coMET 1.2.1
Tiphaine Martin
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/coMET
Last Changed Rev: 115389 / Revision: 116712
Last Changed Date: 2016-03-29 16:13:51 -0700 (Tue, 29 Mar 2016)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: coMET
Version: 1.2.1
Command: rm -rf coMET.buildbin-libdir coMET.Rcheck && mkdir coMET.buildbin-libdir coMET.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=coMET.buildbin-libdir coMET_1.2.1.tar.gz >coMET.Rcheck\00install.out 2>&1 && cp coMET.Rcheck\00install.out coMET-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=coMET.buildbin-libdir --install="check:coMET-install.out" --force-multiarch --no-vignettes --timings coMET_1.2.1.tar.gz
StartedAt: 2016-04-23 01:01:46 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 01:31:16 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 1769.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: coMET.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf coMET.buildbin-libdir coMET.Rcheck && mkdir coMET.buildbin-libdir coMET.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=coMET.buildbin-libdir coMET_1.2.1.tar.gz >coMET.Rcheck\00install.out 2>&1 && cp coMET.Rcheck\00install.out coMET-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=coMET.buildbin-libdir --install="check:coMET-install.out" --force-multiarch --no-vignettes --timings coMET_1.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/coMET.Rcheck'
* using R version 3.2.4 (2016-03-10)
* 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 '1.2.1'
* 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 118.5Mb
  sub-directories of 1Mb or more:
    data     16.1Mb
    doc      41.3Mb
    extdata  60.7Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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'
* 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
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                                        old_size new_size compress
  DNaseI_RoadMapSingle.rda                 240Kb    154Kb       xz
  OtherRegulatoryRegionsAll.rda             12Kb      8Kb       xz
  PancreasIG.rda                            99Kb     76Kb       xz
  PancreasIGtrack.rda                       99Kb     76Kb       xz
  RegulatoryEvidenceBiomartAll.rda          19Kb     13Kb       xz
  RegulatoryEvidenceBiomartMultiple.rda     10Kb      9Kb    bzip2
  allIG.rda                                 99Kb     76Kb       xz
  allIGtrack.rda                            99Kb     76Kb       xz
  allimprintedIG.rda                        99Kb     76Kb       xz
  allimprintedIGtrack.rda                   99Kb     76Kb       xz
  dgfootprints_RoadMapSingle.rda           1.2Mb    110Kb       xz
  dyaRM.rda                                213Kb    132Kb       xz
  enhFANTOMtrack.rda                       567Kb    355Kb       xz
  enhRM.rda                                2.2Mb    1.2Mb       xz
  enhRMtrack.rda                           2.2Mb    1.2Mb       xz
  gcContent.rda                             11Kb      6Kb    bzip2
  gctrack.rda                               11Kb      7Kb    bzip2
  geneENSEMBLtrack.rda                     104Kb     79Kb       xz
  genesENSEMBL.rda                         112Kb     85Kb       xz
  genesGencodetrack.rda                    3.4Mb    2.2Mb       xz
  genetrack4RM.rda                         100Kb     76Kb       xz
  genetrack4psiGTEX.rda                    100Kb     76Kb       xz
  grtrack4eGTex.rda                        3.4Mb    2.2Mb       xz
  imprintedGenesGTEx.rda                    12Kb      9Kb       xz
  interestGenesENSEMBL.rda                 112Kb     85Kb       xz
  interestTranscriptENSEMBL.rda            114Kb     86Kb       xz
  interestgenesENSMBLtrack.rda              98Kb     75Kb       xz
  interesttransENSMBLtrack.rda              98Kb     75Kb       xz
  otherRegulatoryRegionsTrackAll.rda        12Kb      8Kb       xz
  promRMtrack.rda                          312Kb    196Kb       xz
  promRMtrackE063.rda                      240Kb    154Kb       xz
  transENSMBLtrack.rda                     113Kb     84Kb       xz
* 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' ... [439s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
comet.web            21.05   0.23  337.98
coMET-package         6.88   0.42   26.34
chromatinHMMAll_UCSC  5.54   0.01    5.60
imprintedGenes_GTEx   5.38   0.02    5.88
** running examples for arch 'x64' ... [460s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
comet.web            19.44   0.28  331.84
coMET-package        11.78   0.70   31.34
chromatinHMMAll_UCSC  6.69   0.03    6.73
HistoneAll_UCSC       5.91   0.03    5.99
imprintedGenes_GTEx   5.62   0.01    6.10
comet                 5.46   0.02    5.48
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [20s]
 [21s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [23s]
 [23s] 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 WARNING, 5 NOTEs
See
  'D:/biocbld/bbs-3.2-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_1.2.1.zip
* DONE (coMET)

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

nameusersystemelapsed
COSMIC_UCSC0.750.020.81
ChIPTF_ENCODE0.080.000.08
ClinVarCnv_UCSC0.360.010.38
ClinVarMain_UCSC0.450.000.45
CoreillCNV_UCSC0.360.000.36
DNAse_UCSC0.650.000.65
DNaseI_FANTOM0.550.000.55
DNaseI_RoadMap0.390.000.42
GAD_UCSC0.800.000.79
GWAScatalog_UCSC0.530.020.55
GeneReviews_UCSC0.600.000.61
HiCdata2matrix0.070.010.08
HistoneAll_UCSC4.680.004.68
HistoneOne_UCSC0.510.000.51
ISCA_UCSC000
TFBS_FANTOM0.560.020.58
bindingMotifsBiomart_ENSEMBL0.280.010.33
chrUCSC2ENSEMBL000
chromHMM_RoadMap0.920.040.95
chromatinHMMAll_UCSC5.540.015.60
chromatinHMMOne_UCSC0.640.020.65
coMET-package 6.88 0.4226.34
comet3.500.063.56
comet.list1.670.001.66
comet.web 21.05 0.23337.98
cpgIslands_UCSC0.280.000.28
dgfootprints_RoadMap1.080.051.12
eQTL1.430.031.56
eQTL_GTEx2.060.002.06
gcContent_UCSC0.420.010.43
genesName_ENSEMBL0.020.000.02
genes_ENSEMBL1.560.001.56
imprintedGenes_GTEx5.380.025.88
interestGenes_ENSEMBL0.750.000.75
interestTranscript_ENSEMBL1.010.011.03
knownGenes_UCSC1.290.001.30
metQTL1.360.051.41
miRNATargetRegionsBiomart_ENSEMBL0.080.000.08
otherRegulatoryRegionsBiomart_ENSEMBL0.250.000.25
psiQTL_GTEx1.370.021.38
refGenes_UCSC1.400.001.41
regulationBiomart_ENSEMBL0.540.010.56
regulatoryEvidenceBiomart_ENSEMBL0.570.030.60
regulatoryFeaturesBiomart_ENSEMBL0.340.030.37
regulatorySegmentsBiomart_ENSEMBL0.440.020.72
repeatMasker_UCSC0.970.000.96
segmentalDups_UCSC0.620.020.64
snpBiomart_ENSEMBL0.620.000.62
snpLocations_UCSC1.280.001.92
structureBiomart_ENSEMBL0.420.010.62
transcript_ENSEMBL3.230.003.22
xenorefGenes_UCSC0.890.020.91

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

nameusersystemelapsed
COSMIC_UCSC1.450.001.52
ChIPTF_ENCODE0.200.020.22
ClinVarCnv_UCSC0.590.020.61
ClinVarMain_UCSC0.680.000.68
CoreillCNV_UCSC0.610.010.63
DNAse_UCSC1.670.001.67
DNaseI_FANTOM0.880.020.88
DNaseI_RoadMap0.840.040.89
GAD_UCSC0.830.000.83
GWAScatalog_UCSC0.530.000.53
GeneReviews_UCSC0.950.020.96
HiCdata2matrix0.10.00.1
HistoneAll_UCSC5.910.035.99
HistoneOne_UCSC0.590.020.61
ISCA_UCSC000
TFBS_FANTOM0.540.000.55
bindingMotifsBiomart_ENSEMBL0.460.010.47
chrUCSC2ENSEMBL000
chromHMM_RoadMap1.580.051.63
chromatinHMMAll_UCSC6.690.036.73
chromatinHMMOne_UCSC1.230.001.23
coMET-package11.78 0.7031.34
comet5.460.025.48
comet.list2.40.02.4
comet.web 19.44 0.28331.84
cpgIslands_UCSC0.170.012.30
dgfootprints_RoadMap1.170.021.18
eQTL1.980.002.04
eQTL_GTEx1.750.003.06
gcContent_UCSC0.390.020.41
genesName_ENSEMBL000
genes_ENSEMBL1.100.001.11
imprintedGenes_GTEx5.620.016.10
interestGenes_ENSEMBL0.670.020.68
interestTranscript_ENSEMBL0.970.000.97
knownGenes_UCSC1.720.001.71
metQTL1.750.011.95
miRNATargetRegionsBiomart_ENSEMBL0.140.020.16
otherRegulatoryRegionsBiomart_ENSEMBL0.210.010.23
psiQTL_GTEx1.750.021.77
refGenes_UCSC1.410.001.40
regulationBiomart_ENSEMBL0.460.000.47
regulatoryEvidenceBiomart_ENSEMBL0.380.030.40
regulatoryFeaturesBiomart_ENSEMBL0.400.030.44
regulatorySegmentsBiomart_ENSEMBL0.410.050.45
repeatMasker_UCSC0.670.000.67
segmentalDups_UCSC0.610.000.61
snpBiomart_ENSEMBL0.620.010.64
snpLocations_UCSC1.640.001.64
structureBiomart_ENSEMBL0.560.002.48
transcript_ENSEMBL2.550.004.31
xenorefGenes_UCSC0.880.000.89