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CHECK report for sigPathway on malbec2

This page was generated on 2020-10-17 11:55:45 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE sigPathway PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1658/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sigPathway 1.56.0
Weil Lai
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/sigPathway
Branch: RELEASE_3_11
Last Commit: b2b529d
Last Changed Date: 2020-04-27 14:13:29 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: sigPathway
Version: 1.56.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:sigPathway.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings sigPathway_1.56.0.tar.gz
StartedAt: 2020-10-17 05:30:49 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:31:28 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 38.4 seconds
RetCode: 0
Status:  OK 
CheckDir: sigPathway.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:sigPathway.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings sigPathway_1.56.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/sigPathway.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sigPathway/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sigPathway’ version ‘1.56.0’
* 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 ‘sigPathway’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
'library' or 'require' call to ‘XML’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getPathwayStatistics: no visible global function definition for
  ‘na.omit’
getPathwayStatistics: no visible binding for global variable ‘sd’
getPathwayStatistics.NGSk: no visible global function definition for
  ‘na.omit’
gmxToG: no visible global function definition for ‘read.delim’
rankPathways: no visible global function definition for ‘na.omit’
selectGeneSets: no visible global function definition for ‘na.omit’
xmlToG: no visible global function definition for ‘xmlTreeParse’
xmlToG: no visible global function definition for ‘xmlRoot’
xmlToG: no visible global function definition for ‘xmlSize’
xmlToG: no visible global function definition for ‘xmlAttrs’
Undefined global functions or variables:
  na.omit read.delim sd xmlAttrs xmlRoot xmlSize xmlTreeParse
Consider adding
  importFrom("stats", "na.omit", "sd")
  importFrom("utils", "read.delim")
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... NOTE
  Note: found 1 marked Latin-1 string
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
calculate.NGSk 6.838   0.16   7.069
* 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: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/sigPathway.Rcheck/00check.log’
for details.



Installation output

sigPathway.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL sigPathway
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘sigPathway’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c calc_gene_set_internal.c -o calc_gene_set_internal.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c calc_gene_set_stat.c -o calc_gene_set_stat.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c calc_probe_stat.c -o calc_probe_stat.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c calc_weights.c -o calc_weights.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c matrix_fn.c -o matrix_fn.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c permute.c -o permute.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c shuffle.c -o shuffle.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c sigPathway.c -o sigPathway.o
gcc -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o sigPathway.so calc_gene_set_internal.o calc_gene_set_stat.o calc_probe_stat.o calc_weights.o matrix_fn.o permute.o shuffle.o sigPathway.o -L/home/biocbuild/bbs-3.11-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.11-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-sigPathway/00new/sigPathway/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (sigPathway)

Tests output


Example timings

sigPathway.Rcheck/sigPathway-Ex.timings

nameusersystemelapsed
calcTStatFast0.1830.0040.187
calculate.NGSk6.8380.1607.069
calculatePathwayStatistics3.3620.0483.410
estimateNumPerm0.0020.0000.002
runSigPathway3.7090.0403.749