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CHECK report for geneXtendeR on malbec1

This page was generated on 2020-04-15 12:11:55 -0400 (Wed, 15 Apr 2020).

Package 670/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
geneXtendeR 1.12.0
Bohdan Khomtchouk
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/geneXtendeR
Branch: RELEASE_3_10
Last Commit: 2b766f5
Last Changed Date: 2019-10-29 13:10:08 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: geneXtendeR
Version: 1.12.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:geneXtendeR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings geneXtendeR_1.12.0.tar.gz
StartedAt: 2020-04-15 04:14:32 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 04:53:43 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 2350.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: geneXtendeR.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:geneXtendeR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings geneXtendeR_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/geneXtendeR.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘geneXtendeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘geneXtendeR’ version ‘1.12.0’
* package encoding: UTF-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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘geneXtendeR’ can be installed ... WARNING
Found the following significant warnings:
  annotate.c:106:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  annotate.c:116:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  extract_number.c:98:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  extract_number.c:108:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  extract_peaks.c:107:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  extract_peaks.c:117:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/home/biocbuild/bbs-3.10-bioc/meat/geneXtendeR.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 11.5Mb
  sub-directories of 1Mb or more:
    data      5.8Mb
    doc       1.9Mb
    extdata   3.5Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘rtracklayer’
A package should be listed in only one of these fields.
* 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
Namespaces in Imports field not imported from:
  ‘BiocStyle’ ‘SnowballC’ ‘org.Rn.eg.db’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.geneXtender: no visible binding for global variable ‘type’
.geneXtender: no visible binding for global variable ‘seqid’
.geneXtender: no visible binding for global variable ‘gene_id’
.geneXtender: no visible binding for global variable ‘gene_name’
annotate_n: no visible binding for global variable ‘..I’
annotate_n: no visible binding for global variable ‘seqid’
diffGO: no visible binding for global variable ‘rat’
gene_annotate: no visible global function definition for ‘.’
gene_annotate: no visible binding for global variable
  ‘Distance-of-Gene-to-Nearest-Peak’
gene_annotate: no visible global function definition for ‘sd’
gene_annotate: no visible binding for global variable ‘Chromosome’
gene_annotate: no visible binding for global variable ‘Gene-Start’
gene_annotate: no visible binding for global variable ‘Gene-End’
gene_annotate: no visible binding for global variable ‘Gene-ID’
gene_annotate: no visible binding for global variable ‘Gene-Name’
gene_annotate: no visible binding for global variable
  ‘Peaks-on-Gene-Body’
gene_annotate: no visible binding for global variable
  ‘Number-of-Peaks-Associated-with-Gene’
gene_lookup: no visible binding for global variable ‘gene_name_id’
gene_lookup: no visible binding for global variable ‘gene_id’
gene_lookup : internal_find: no visible binding for global variable
  ‘Chromosome’
gene_lookup : internal_find: no visible binding for global variable
  ‘distance’
gene_lookup : internal_find: no visible global function definition for
  ‘na.omit’
gene_lookup: no visible binding for global variable ‘..I’
gene_lookup: no visible binding for global variable ‘distance’
makeWordCloud: no visible binding for global variable ‘rat’
meanPeakLength: no visible binding for global variable ‘rat’
peaksInput: no visible binding for global variable ‘chr’
peaksInput: no visible global function definition for ‘na.omit’
peaksMerge: no visible binding for global variable ‘chr’
peaksMerge: no visible binding for global variable ‘g’
peaksMerge: no visible global function definition for ‘.’
plotWordFreq : geneXtender: no visible binding for global variable
  ‘type’
plotWordFreq : geneXtender: no visible binding for global variable
  ‘seqid’
plotWordFreq : geneXtender: no visible binding for global variable
  ‘gene_id’
plotWordFreq : geneXtender: no visible binding for global variable
  ‘gene_name’
Undefined global functions or variables:
  . ..I Chromosome Distance-of-Gene-to-Nearest-Peak Gene-End Gene-ID
  Gene-Name Gene-Start Number-of-Peaks-Associated-with-Gene
  Peaks-on-Gene-Body chr distance g gene_id gene_name gene_name_id
  na.omit rat sd seqid type
Consider adding
  importFrom("stats", "na.omit", "sd")
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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... NOTE
Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/geneXtendeR.Rnw’
(Is a VignetteBuilder field missing?)
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
meanPeakLengthPlot 55.876  0.300  55.174
hotspotPlot        47.656  0.532  39.893
barChart           30.768  0.312  30.059
cumlinePlot        28.440  0.220  27.604
linePlot           27.760  0.184  26.773
meanPeakLength     27.584  0.168  23.744
annotate           25.752  0.364  24.761
plotWordFreq       24.880  0.456  24.016
makeNetwork        24.132  0.208  24.216
gene_annotate      23.688  0.452  24.477
peakLengthBoxplot  23.112  0.168  21.795
diffGO             22.224  0.276  22.983
distinct           21.996  0.124  20.762
makeWordCloud      21.320  0.228  19.868
gene_lookup        16.556  0.212  17.654
peaksMerge          6.836  0.040   1.982
peaksInput          6.500  0.176   4.500
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 6 NOTEs
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/geneXtendeR.Rcheck/00check.log’
for details.



Installation output

geneXtendeR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL geneXtendeR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘geneXtendeR’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c annotate.c -o annotate.o
annotate.c: In function ‘annotate’:
annotate.c:106:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
     fgets(varstr, 50000, varfp);
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
annotate.c:116:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
     fgets(vcfstr, 10000, vcffp);
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c extract_number.c -o extract_number.o
extract_number.c: In function ‘extractnumber’:
extract_number.c:72:10: warning: variable ‘n_1’ set but not used [-Wunused-but-set-variable]
     long n_1;
          ^~~
extract_number.c:66:10: warning: variable ‘j_1’ set but not used [-Wunused-but-set-variable]
     long j_1;
          ^~~
extract_number.c:54:12: warning: variable ‘pvcfcol5_5’ set but not used [-Wunused-but-set-variable]
     char * pvcfcol5_5;
            ^~~~~~~~~~
extract_number.c:53:12: warning: variable ‘pvcfcol4_4’ set but not used [-Wunused-but-set-variable]
     char * pvcfcol4_4;
            ^~~~~~~~~~
extract_number.c:52:12: warning: variable ‘pvcfcol3_3’ set but not used [-Wunused-but-set-variable]
     char * pvcfcol3_3;
            ^~~~~~~~~~
extract_number.c:51:12: warning: variable ‘pvcfcol2_2’ set but not used [-Wunused-but-set-variable]
     char * pvcfcol2_2;
            ^~~~~~~~~~
extract_number.c:50:12: warning: variable ‘pvcfcol1_1’ set but not used [-Wunused-but-set-variable]
     char * pvcfcol1_1;
            ^~~~~~~~~~
extract_number.c:98:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
     fgets(varstr, 50000, varfp);
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
extract_number.c:108:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
     fgets(vcfstr, 10000, vcffp);
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c extract_peaks.c -o extract_peaks.o
extract_peaks.c: In function ‘extractpeaks’:
extract_peaks.c:107:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
     fgets(varstr, 50000, varfp);
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
extract_peaks.c:117:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
     fgets(vcfstr, 10000, vcffp);
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.10-bioc/R/lib -L/usr/local/lib -o geneXtendeR.so annotate.o extract_number.o extract_peaks.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-geneXtendeR/00new/geneXtendeR/libs
** R
** data
*** moving datasets to lazyload DB
** 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 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 (geneXtendeR)

Tests output

geneXtendeR.Rcheck/tests/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(geneXtendeR)
Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, 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, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


> 
> test_check("geneXtendeR")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 86 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
    user   system  elapsed 
6428.648   37.316 1669.769 

Example timings

geneXtendeR.Rcheck/geneXtendeR-Ex.timings

nameusersystemelapsed
allPeakLengths0.0240.0040.070
annotate25.752 0.36424.761
annotate_n000
barChart30.768 0.31230.059
cumlinePlot28.440 0.22027.604
diffGO22.224 0.27622.983
distinct21.996 0.12420.762
gene_annotate23.688 0.45224.477
gene_lookup16.556 0.21217.654
hotspotPlot47.656 0.53239.893
linePlot27.760 0.18426.773
makeNetwork24.132 0.20824.216
makeWordCloud21.320 0.22819.868
meanPeakLength27.584 0.16823.744
meanPeakLengthPlot55.876 0.30055.174
peakLengthBoxplot23.112 0.16821.795
peaksInput6.5000.1764.500
peaksMerge6.8360.0401.982
plotWordFreq24.880 0.45624.016
rat4.4520.2044.680
samplepeaksinput0.2080.0000.063