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BioC 3.5: CHECK report for genoset on veracruz2

This page was generated on 2017-10-18 14:29:27 -0400 (Wed, 18 Oct 2017).

Package 546/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genoset 1.32.0
Peter M. Haverty
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/genoset
Branch: RELEASE_3_5
Last Commit: d210aa8
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  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: genoset
Version: 1.32.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genoset_1.32.0.tar.gz
StartedAt: 2017-10-18 04:11:14 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 04:13:46 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 152.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: genoset.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genoset_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/genoset.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 ‘genoset/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genoset’ version ‘1.32.0’
* 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 ‘genoset’ 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
Unexported object imported by a ':::' call: ‘BiocGenerics:::testPackage’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function calls to a different package:
  .Call("RleViews_viewMaxs", ..., PACKAGE = "IRanges")
  .Call("RleViews_viewMeans", ..., PACKAGE = "IRanges")
  .Call("RleViews_viewMins", ..., PACKAGE = "IRanges")
  .Call("RleViews_viewSums", ..., PACKAGE = "IRanges")
  .Call("RleViews_viewWhichMaxs", ..., PACKAGE = "IRanges")
  .Call("RleViews_viewWhichMins", ..., PACKAGE = "IRanges")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* 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 ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'GenoSet,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘prove.R’
  Comparing ‘prove.Rout’ to ‘prove.Rout.save’ ...15c15
<     IQR, mad, sd, var, xtabs
---
>     IQR, mad, xtabs
20,32c20,24
<     as.data.frame, cbind, colMeans, colSums, colnames, do.call,
<     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
<     lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
<     pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
<     setdiff, sort, table, tapply, union, unique, unsplit, which,
<     which.max, which.min
< 
< 
< Attaching package: 'S4Vectors'
< 
< The following object is masked from 'package:base':
< 
<     expand.grid
---
>     as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
>     eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply,
>     mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
>     rank, rbind, rep.int, rownames, sapply, setdiff, sort, table,
>     tapply, union, unique, unlist, unsplit
41,57c33,37
< Attaching package: 'matrixStats'
< 
< The following objects are masked from 'package:Biobase':
< 
<     anyMissing, rowMedians
< 
< 
< Attaching package: 'DelayedArray'
< 
< The following objects are masked from 'package:matrixStats':
< 
<     colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
< 
< The following object is masked from 'package:base':
< 
<     apply
< 
---
> *** Genoset API Changes ***
> The genoset class is transitioning to extending 
> RangedSummarizedExperiment rather than eSet. For this release, 
> please use the RSE API as the eSet API has been deprecated
>  (e.g. colnames instead of sampleNames). ***
73d52
< Working on segmentation for sample number 2 : a2
74a54
> Working on segmentation for sample number 2 : a2
77c57
< RUNIT TEST PROTOCOL -- Wed Oct 18 04:13:42 2017 
---
> RUNIT TEST PROTOCOL -- Sat Sep 12 10:57:59 2015 
79c59
< Number of test functions: 32 
---
> Number of test functions: 36 
85,86c65,66
< genoset RUnit Tests - 32 test functions, 0 errors, 0 failures
< Number of test functions: 32 
---
> genoset RUnit Tests - 36 test functions, 0 errors, 0 failures
> Number of test functions: 36 
88a69
> There were 19 warnings (use warnings() to see them)
 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, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/genoset.Rcheck/00check.log’
for details.


genoset.Rcheck/00install.out:

* installing *source* package ‘genoset’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c bounds.c -o bounds.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.c -o init.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c rangeSummaries.c -o rangeSummaries.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c utils.c -o utils.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o genoset.so bounds.o init.o rangeSummaries.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/genoset.Rcheck/genoset/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (genoset)

genoset.Rcheck/genoset-Ex.timings:

nameusersystemelapsed
GenoSet-class0.3120.0180.344
RleDataFrame-class0.8680.0130.937
RleDataFrame-views0.0350.0030.039
baf2mbaf0.0240.0060.030
boundingIndices0.0010.0010.002
calcGC000
calcGC20.0010.0000.001
chr-methods0.0160.0080.024
chrIndices-methods0.0120.0040.017
chrInfo-methods0.0370.0080.046
chrNames-methods0.0300.0070.038
chrOrder0.0010.0000.001
gcCorrect0.0020.0010.003
genoPlot-methods0.0510.0110.063
genoPos-methods0.0180.0060.025
genome0.0710.0060.077
genomeAxis0.0250.0040.029
genoset-methods0.0780.0010.080
genoset-subset0.2350.0090.250
isGenomeOrder0.0160.0050.021
modeCenter0.0040.0010.005
pos-methods0.0110.0090.021
rangeSampleMeans0.0220.0050.027
readGenoSet0.0000.0000.001
runCBS1.0020.0101.031
segPairTable-methods0.0070.0000.008
segTable-methods0.7490.0110.784
segs2Rle0.6680.0090.692
segs2RleDataFrame0.6260.0080.643
toGenomeOrder0.0430.0040.047