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BioC 3.4: CHECK report for DEGreport on zin1

This page was generated on 2016-09-21 03:39:03 -0700 (Wed, 21 Sep 2016).

Package 303/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DEGreport 1.9.8
Lorena Pantano
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DEGreport
Last Changed Rev: 119734 / Revision: 121152
Last Changed Date: 2016-07-29 10:13:43 -0700 (Fri, 29 Jul 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DEGreport
Version: 1.9.8
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings DEGreport_1.9.8.tar.gz
StartedAt: 2016-09-20 05:27:17 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 05:28:34 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 76.5 seconds
RetCode: 0
Status:  OK 
CheckDir: DEGreport.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings DEGreport_1.9.8.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/DEGreport.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DEGreport/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DEGreport’ version ‘1.9.8’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DEGreport’ 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 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
.convertIDs: no visible global function definition for ‘keys’
.mds: no visible binding for global variable ‘one’
.mds: no visible binding for global variable ‘two’
.mds: no visible binding for global variable ‘label’
.plot_base: no visible binding for global variable ‘value’
.plot_base: no visible binding for global variable ‘variable’
.plot_cluster: no visible binding for global variable ‘x’
.plot_cluster: no visible binding for global variable ‘value’
.plot_cluster: no visible binding for global variable ‘group’
.run_cluster_profiler: no visible global function definition for
  ‘enrichGO’
.run_cluster_profiler: no visible global function definition for
  ‘print_enrichGO’
.table_w_fc: no visible global function definition for ‘colData’
.table_w_fc : <anonymous>: no visible global function definition for
  ‘results’
.table_w_fc : <anonymous>: no visible binding for global variable
  ‘log2FoldChange’
.table_w_fc: no visible binding for global variable ‘comp’
.table_w_fc: no visible binding for global variable ‘log2FoldChange’
degBI: no visible global function definition for ‘bplapply’
degBI: no visible global function definition for ‘MulticoreParam’
degBIcmd: no visible global function definition for ‘jags.model’
degBIcmd: no visible global function definition for ‘coda.samples’
degResults: no visible global function definition for ‘assay’
degResults: no visible global function definition for ‘rlog’
degResults: no visible global function definition for ‘results’
degResults: no visible global function definition for ‘colData’
degResults: no visible global function definition for ‘rowMax’
degVolcano: no visible binding for global variable ‘logFC’
degVolcano: no visible binding for global variable ‘V1’
degVolcano: no visible binding for global variable ‘V2’
degVolcano: no visible binding for global variable ‘adj.P.Val’
degVolcano: no visible binding for global variable ‘x’
degVolcano: no visible binding for global variable ‘y’
figurepvaluebyvarexp: possible error in degMV(g1, g2, pvalues, counts):
  unused argument (counts)
plot_top: no visible global function definition for ‘colData’
plot_top : <anonymous>: no visible global function definition for
  ‘plotCounts’
plot_top : <anonymous>: no visible binding for global variable ‘count’
plot_top : <anonymous>: no visible binding for global variable
  ‘treatment’
Undefined global functions or variables:
  MulticoreParam V1 V2 adj.P.Val assay bplapply coda.samples colData
  comp count enrichGO group jags.model keys label log2FoldChange logFC
  one plotCounts print_enrichGO results rlog rowMax treatment two value
  variable x y
* 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 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
degResults 13.044    0.1  13.152
* 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 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/DEGreport.Rcheck/00check.log’
for details.


DEGreport.Rcheck/00install.out:

* installing *source* package ‘DEGreport’ ...
** 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 (DEGreport)

DEGreport.Rcheck/DEGreport-Ex.timings:

nameusersystemelapsed
degMB0.3360.0000.338
degMV0.3560.0080.367
degMean0.2600.0040.263
degObj0.0040.0040.005
degPR0.1520.0000.153
degPatterns0.8000.0000.798
degRank0.0040.0000.005
degResults13.044 0.10013.152
degVB0.3000.0080.307
degVar0.2840.0000.286
degVolcano0.6000.0000.602