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BioC 3.4: CHECK report for coMET on malbec1

This page was generated on 2017-04-15 16:12:40 -0400 (Sat, 15 Apr 2017).

Package 247/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
coMET 1.6.0
Tiphaine Martin
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/coMET
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: coMET
Version: 1.6.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings coMET_1.6.0.tar.gz
StartedAt: 2017-04-14 21:44:24 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 21:56:53 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 748.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: coMET.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings coMET_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/coMET.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘coMET/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘coMET’ version ‘1.6.0’
* 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 for sufficient/correct file permissions ... 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 ‘/home/biocbuild/bbs-3.4-bioc/meat/coMET.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 17.3Mb
  sub-directories of 1Mb or more:
    data      9.7Mb
    doc       2.6Mb
    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
* 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 ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
comet.web     18.260  0.180 356.428
coMET-package  3.552  0.032  30.222
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/home/biocbuild/bbs-3.4-bioc/meat/coMET.Rcheck/00check.log’
for details.


coMET.Rcheck/00install.out:

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
* DONE (coMET)

coMET.Rcheck/coMET-Ex.timings:

nameusersystemelapsed
COSMIC_UCSC0.6480.0000.650
ChIPTF_ENCODE0.0680.0040.071
ClinVarCnv_UCSC0.3320.0000.332
ClinVarMain_UCSC0.3520.0040.354
CoreillCNV_UCSC0.3200.0040.324
DNAse_UCSC0.4080.0000.407
DNaseI_FANTOM0.4760.0000.476
DNaseI_RoadMap0.3400.0000.342
GAD_UCSC0.3520.0000.352
GWAScatalog_UCSC0.3000.0040.301
GeneReviews_UCSC0.5200.0000.519
HiCdata2matrix0.0240.0040.028
HistoneAll_UCSC3.1760.0003.174
HistoneOne_UCSC0.3160.0040.319
ISCA_UCSC0.0000.0000.001
TFBS_FANTOM0.320.000.32
bindingMotifsBiomart_ENSEMBL0.2120.0040.216
chrUCSC2ENSEMBL000
chromHMM_RoadMap0.8160.0000.817
chromatinHMMAll_UCSC4.0560.0244.085
chromatinHMMOne_UCSC0.4840.0000.485
coMET-package 3.552 0.03230.222
comet2.5960.0082.608
comet.list0.8880.0000.889
comet.web 18.260 0.180356.428
cpgIslands_UCSC0.1840.0040.191
dgfootprints_RoadMap0.6160.0040.620
eQTL0.9040.0000.907
eQTL_GTEx1.0800.0041.084
gcContent_UCSC0.1880.0000.189
genesName_ENSEMBL0.0040.0000.004
genes_ENSEMBL0.6400.0000.637
imprintedGenes_GTEx3.5480.0044.007
interestGenes_ENSEMBL0.5240.0000.523
interestTranscript_ENSEMBL0.6520.0000.651
knownGenes_UCSC0.8200.0000.819
metQTL0.8280.0000.829
miRNATargetRegionsBiomart_ENSEMBL0.0880.0000.086
otherRegulatoryRegionsBiomart_ENSEMBL0.1320.0000.131
psiQTL_GTEx0.8360.0040.840
refGenes_UCSC0.7800.0000.778
regulationBiomart_ENSEMBL0.2280.0000.226
regulatoryEvidenceBiomart_ENSEMBL0.1800.0000.182
regulatoryFeaturesBiomart_ENSEMBL0.2200.0000.219
regulatorySegmentsBiomart_ENSEMBL0.1880.0040.190
repeatMasker_UCSC0.4440.0000.444
segmentalDups_UCSC0.3040.0000.301
snpBiomart_ENSEMBL0.3680.0000.367
snpLocations_UCSC0.8680.0040.872
structureBiomart_ENSEMBL0.2920.0000.291
transcript_ENSEMBL1.5320.0081.541
xenorefGenes_UCSC0.4480.0000.446