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BioC 3.4: CHECK report for MetCirc on malbec1

This page was generated on 2017-04-15 16:13:54 -0400 (Sat, 15 Apr 2017).

Package 751/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MetCirc 1.0.1
Thomas Naake
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/MetCirc
Last Changed Rev: 125354 / Revision: 128728
Last Changed Date: 2016-12-20 15:35:47 -0500 (Tue, 20 Dec 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: MetCirc
Version: 1.0.1
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings MetCirc_1.0.1.tar.gz
StartedAt: 2017-04-14 23:46:15 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 23:47:40 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 85.9 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: MetCirc.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings MetCirc_1.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/MetCirc.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 ‘MetCirc/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MetCirc’ version ‘1.0.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘MetCirc’ 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 ... NOTE
Unexported object imported by a ':::' call: ‘circlize:::get.sector.data’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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
  binnedMSP.RData               34Kb     20Kb    bzip2
  idMSMStissueproject.RData    141Kb     88Kb       xz
  idMSMStoMSP.RData             57Kb     19Kb       xz
  sd01_outputXCMS.RData        1.4Mb    1.0Mb       xz
  sd02_deconvoluted.RData       51Kb     46Kb       xz
  similarityMat.RData          516Kb    221Kb       xz
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... 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
allocatePrecursor2mz 5.756  0.108    5.87
* 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: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/MetCirc.Rcheck/00check.log’
for details.


MetCirc.Rcheck/00install.out:

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

MetCirc.Rcheck/MetCirc-Ex.timings:

nameusersystemelapsed
NDP0.0360.0000.035
allocatePrecursor2mz5.7560.1085.870
binning2.0080.1802.191
cart2Polar000
circosLegend0.5840.0000.586
combine0.6080.0000.606
convert2MSP0.2920.0000.294
createLink0Matrix0.1120.0000.113
createLinkMatrix0.7840.0000.786
createOrderedSimMat0.9000.1761.077
createSimilarityMatrix0.0720.0040.078
cutLinkMatrix0.7160.0000.716
cutUniquePreMZ0.0000.0040.000
extract-methods0.2680.0000.269
getBegEndIndMSP0.2720.0000.271
getLinkMatrixIndices000
getMSP0.3480.0400.386
getMetaboliteClass0.2880.0040.293
getMetaboliteName0.3000.0000.301
getName0.2800.0000.282
getPrecursorMZ0.3360.0000.337
getRT0.2920.0000.294
highlight2.5040.0002.506
length-method0.3640.0040.371
minFragCart2Polar1.7640.0001.763
msp2FunctionalLossesMSP0.3840.0000.384
plotCircos2.4760.0002.479
printInformationHover1.1400.0001.142
setMetaboliteClass0.320.000.32
setMetaboliteName0.2720.0000.272
setName0.3160.0000.318
shinyCircos0.6520.0000.655
show-method0.2560.0000.260
thresholdLinkMatrix0.7240.0000.728
truncateName000