Back to Multiple platform build/check report for BioC 3.15
ABCDEF[G]HIJKLMNOPQRSTUVWXYZ

This page was generated on 2022-08-08 13:19:32 -0400 (Mon, 08 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4362
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4180
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for geneXtendeR on nebbiolo1


To the developers/maintainers of the geneXtendeR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/geneXtendeR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 761/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
geneXtendeR 1.22.0  (landing page)
Bohdan Khomtchouk
Snapshot Date: 2022-08-07 13:55:12 -0400 (Sun, 07 Aug 2022)
git_url: https://git.bioconductor.org/packages/geneXtendeR
git_branch: RELEASE_3_15
git_last_commit: 36e8d12
git_last_commit_date: 2022-04-26 11:36:15 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: geneXtendeR
Version: 1.22.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:geneXtendeR.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings geneXtendeR_1.22.0.tar.gz
StartedAt: 2022-08-07 20:08:30 -0400 (Sun, 07 Aug 2022)
EndedAt: 2022-08-07 20:18:57 -0400 (Sun, 07 Aug 2022)
EllapsedTime: 627.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: geneXtendeR.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:geneXtendeR.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings geneXtendeR_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/geneXtendeR.Rcheck’
* using R version 4.2.1 (2022-06-23)
* 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 ‘1.22.0’
* 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-3.15-bioc/meat/geneXtendeR.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  9.9Mb
  sub-directories of 1Mb or more:
    data      5.8Mb
    doc       1.8Mb
    extdata   2.1Mb
* 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 LazyData ... WARNING
  LazyData DB of 5.8 MB without LazyDataCompression set
  See §1.1.6 of 'Writing R Extensions'
* 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 (user + system) or elapsed time > 5s
                     user system elapsed
meanPeakLengthPlot 31.366  0.620  34.422
hotspotPlot        21.199  0.467  23.909
annotate           15.392  1.781  19.737
barChart           15.416  0.795  18.591
cumlinePlot        15.603  0.568  18.587
linePlot           15.055  0.264  17.825
gene_annotate      14.161  0.220  16.790
distinct           12.197  0.287  14.883
makeWordCloud      11.939  0.194  14.453
makeNetwork        11.294  0.237  13.958
diffGO             10.686  0.433  13.562
meanPeakLength     10.409  0.181  12.984
plotWordFreq       10.100  0.196  12.624
peakLengthBoxplot   9.725  0.176  12.472
gene_lookup         9.087  0.204  11.629
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 6 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/geneXtendeR.Rcheck/00check.log’
for details.



Installation output

geneXtendeR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL geneXtendeR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘geneXtendeR’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.15-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]
  106 |     fgets(varstr, 50000, varfp);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
annotate.c:116:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  116 |     fgets(vcfstr, 10000, vcffp);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.15-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]
   72 |     long n_1;
      |          ^~~
extract_number.c:66:10: warning: variable ‘j_1’ set but not used [-Wunused-but-set-variable]
   66 |     long j_1;
      |          ^~~
extract_number.c:54:12: warning: variable ‘pvcfcol5_5’ set but not used [-Wunused-but-set-variable]
   54 |     char * pvcfcol5_5;
      |            ^~~~~~~~~~
extract_number.c:53:12: warning: variable ‘pvcfcol4_4’ set but not used [-Wunused-but-set-variable]
   53 |     char * pvcfcol4_4;
      |            ^~~~~~~~~~
extract_number.c:52:12: warning: variable ‘pvcfcol3_3’ set but not used [-Wunused-but-set-variable]
   52 |     char * pvcfcol3_3;
      |            ^~~~~~~~~~
extract_number.c:51:12: warning: variable ‘pvcfcol2_2’ set but not used [-Wunused-but-set-variable]
   51 |     char * pvcfcol2_2;
      |            ^~~~~~~~~~
extract_number.c:50:12: warning: variable ‘pvcfcol1_1’ set but not used [-Wunused-but-set-variable]
   50 |     char * pvcfcol1_1;
      |            ^~~~~~~~~~
extract_number.c:98:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
   98 |     fgets(varstr, 50000, varfp);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
extract_number.c:108:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  108 |     fgets(vcfstr, 10000, vcffp);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.15-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]
  107 |     fgets(varstr, 50000, varfp);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
extract_peaks.c:117:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  117 |     fgets(vcfstr, 10000, vcffp);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.15-bioc/R/lib -L/usr/local/lib -o geneXtendeR.so annotate.o extract_number.o extract_peaks.o -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.15-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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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

Attaching package: 'BiocGenerics'

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.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 86 ]
> 
> proc.time()
   user  system elapsed 
138.328   6.205 143.920 

Example timings

geneXtendeR.Rcheck/geneXtendeR-Ex.timings

nameusersystemelapsed
allPeakLengths0.0480.0000.051
annotate15.392 1.78119.737
annotate_n000
barChart15.416 0.79518.591
cumlinePlot15.603 0.56818.587
diffGO10.686 0.43313.562
distinct12.197 0.28714.883
gene_annotate14.161 0.22016.790
gene_lookup 9.087 0.20411.629
hotspotPlot21.199 0.46723.909
linePlot15.055 0.26417.825
makeNetwork11.294 0.23713.958
makeWordCloud11.939 0.19414.453
meanPeakLength10.409 0.18112.984
meanPeakLengthPlot31.366 0.62034.422
peakLengthBoxplot 9.725 0.17612.472
peaksInput0.2160.0300.237
peaksMerge0.1450.0040.126
plotWordFreq10.100 0.19612.624
rat2.7150.2522.967
samplepeaksinput0.0070.0000.007