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BioC 3.5: CHECK report for ELMER on veracruz2

This page was generated on 2017-10-18 14:33:21 -0400 (Wed, 18 Oct 2017).

Package 396/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ELMER 1.6.0
Simon Coetzee
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/ELMER
Branch: RELEASE_3_5
Last Commit: 6ca47b6
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ELMER
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ELMER_1.6.0.tar.gz
StartedAt: 2017-10-18 03:09:06 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 03:14:54 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 348.3 seconds
RetCode: 0
Status:  OK 
CheckDir: ELMER.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ELMER_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/ELMER.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ELMER/DESCRIPTION’ ... OK
* this is package ‘ELMER’ version ‘1.6.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘ELMER’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
* 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘ELMER.data’ ‘Homo.sapiens’
  ‘IlluminaHumanMethylation450kanno.ilmn12.hg19’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Stat.diff.meth: no visible binding for global variable ‘t.test’
Stat.nonpara : <anonymous>: no visible global function definition for
  ‘wilcox.test’
Stat.nonpara: no visible global function definition for ‘wilcox.test’
Stat.nonpara.permu : <anonymous>: no visible global function definition
  for ‘wilcox.test’
Stat.nonpara.permu: no visible global function definition for
  ‘write.table’
TCGA.pipe: no visible global function definition for ‘read.csv’
TCGA.pipe: no visible global function definition for ‘write.csv’
TF.rank.plot: no visible global function definition for ‘data’
TF.rank.plot: no visible binding for global variable ‘pvalue’
TF.rank.plot: no visible binding for global variable ‘label’
TF.rank.plot: no visible global function definition for ‘pdf’
TF.rank.plot: no visible global function definition for ‘dev.off’
fetch.pair: no visible global function definition for ‘read.csv’
get.TFs: no visible global function definition for ‘data’
get.TFs: no visible global function definition for ‘read.csv’
get.TFs: no visible global function definition for ‘write.csv’
get.diff.meth: no visible global function definition for ‘p.adjust’
get.diff.meth: no visible global function definition for ‘write.csv’
get.enriched.motif: no visible global function definition for ‘data’
get.enriched.motif: no visible global function definition for
  ‘write.csv’
get.enriched.motif: no visible global function definition for
  ‘read.csv’
get.feature.probe: no visible binding for global variable
  ‘IlluminaHumanMethylation450kanno.ilmn12.hg19’
get.feature.probe: no visible global function definition for ‘data’
get.pair: no visible global function definition for ‘write.csv’
get.pair : <anonymous>: no visible global function definition for
  ‘t.test’
get.pair : <anonymous>: no visible global function definition for
  ‘wilcox.test’
get.permu : <anonymous>: no visible global function definition for
  ‘read.table’
lm_eqn: no visible global function definition for ‘lm’
lm_eqn: no visible global function definition for ‘coef’
matrixClinic: no visible global function definition for ‘read.delim’
matrixMeth: no visible global function definition for ‘read.table’
matrixMeth : <anonymous>: no visible global function definition for
  ‘read.table’
matrixRNA: no visible global function definition for ‘read.table’
matrixRNA : <anonymous>: no visible global function definition for
  ‘read.table’
motif.enrichment.plot: no visible global function definition for
  ‘read.csv’
motif.enrichment.plot: no visible binding for global variable ‘upperOR’
motif.enrichment.plot: no visible binding for global variable ‘lowerOR’
motif.enrichment.plot: no visible binding for global variable ‘motif’
motif.enrichment.plot: no visible binding for global variable ‘OR’
promoterMeth: no visible global function definition for ‘write.csv’
scatter: no visible binding for global variable ‘value’
schematic: no visible global function definition for ‘pdf’
schematic: no visible global function definition for ‘dev.off’
txs: no visible binding for global variable ‘Homo.sapiens’
show,MEE.data: no visible global function definition for ‘str’
show,Pair: no visible global function definition for ‘str’
summary,MEE.data: no visible global function definition for ‘str’
summary,Pair: no visible global function definition for ‘str’
Undefined global functions or variables:
  Homo.sapiens IlluminaHumanMethylation450kanno.ilmn12.hg19 OR coef
  data dev.off label lm lowerOR motif p.adjust pdf pvalue read.csv
  read.delim read.table str t.test upperOR value wilcox.test write.csv
  write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("stats", "coef", "lm", "p.adjust", "t.test", "wilcox.test")
  importFrom("utils", "data", "read.csv", "read.delim", "read.table",
             "str", "write.csv", "write.table")
to your NAMESPACE file.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* 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
scatter.plot   9.243  0.072   9.652
GetNearGenes   7.002  0.257   7.426
schematic.plot 7.107  0.148   7.480
get.pair       5.881  0.250   6.300
fetch.pair     5.335  0.148   5.628
* 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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/ELMER.Rcheck/00check.log’
for details.


ELMER.Rcheck/00install.out:

* installing *source* package ‘ELMER’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ELMER)

ELMER.Rcheck/ELMER-Ex.timings:

nameusersystemelapsed
GetNearGenes7.0020.2577.426
TCGA.pipe0.0010.0000.000
TF.rank.plot1.6000.0781.722
fetch.mee1.7290.0131.796
fetch.pair5.3350.1485.628
get.TFs1.1270.0231.181
get.diff.meth0.3010.0070.317
get.enriched.motif3.2640.2793.631
get.feature.probe1.9640.2542.263
get.pair5.8810.2506.300
get.permu4.6340.1404.907
getExp0.6640.0080.688
getGeneID3.7140.1333.963
getGeneInfo4.4290.1834.728
getMeth0.6870.0050.710
getPair0.0030.0010.003
getProbeInfo0.6920.0030.710
getSample0.6630.0040.683
getSymbol3.8040.1494.059
getTCGA0.0210.0150.903
motif.enrichment.plot0.5440.0020.553
promoterMeth0.2000.0060.209
scatter.plot9.2430.0729.652
schematic.plot7.1070.1487.480
txs4.1500.1594.502