Back to Multiple platform build/check report for BioC 3.20:   simplified   long
ABCDEF[G]HIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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

Package 811/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
geneXtendeR 1.32.0  (landing page)
Bohdan Khomtchouk
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/geneXtendeR
git_branch: RELEASE_3_20
git_last_commit: 94a7410
git_last_commit_date: 2024-10-29 10:14:40 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


CHECK results for geneXtendeR on kunpeng2

To the developers/maintainers of the geneXtendeR package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: geneXtendeR
Version: 1.32.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:geneXtendeR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings geneXtendeR_1.32.0.tar.gz
StartedAt: 2024-11-20 08:08:28 -0000 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 08:34:59 -0000 (Wed, 20 Nov 2024)
EllapsedTime: 1590.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: geneXtendeR.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:geneXtendeR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings geneXtendeR_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/geneXtendeR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘geneXtendeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘geneXtendeR’ version ‘1.32.0’
* 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:159:79: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
  annotate.c:191:87: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
  annotate.c:199:87: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
  annotate.c:208:87: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
  annotate.c:228:83: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
  extract_peaks.c:202:79: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
See ‘/home/biocbuild/bbs-3.20-bioc/meat/geneXtendeR.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’
* checking installed package size ... NOTE
  installed size is 11.6Mb
  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 code 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
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 44.195  0.668  96.554
hotspotPlot        23.638  0.370  43.665
annotate           20.397  0.645  32.090
barChart           20.086  0.635  31.684
cumlinePlot        19.759  0.430  33.566
linePlot           19.558  0.340  56.185
gene_annotate      16.688  0.221  47.238
makeNetwork        15.119  0.619 154.650
makeWordCloud      15.290  0.295 233.850
distinct           14.986  0.216  27.705
diffGO             14.538  0.414  26.662
plotWordFreq       14.304  0.254  31.762
peakLengthBoxplot  13.777  0.104  29.491
meanPeakLength     13.354  0.236 127.736
gene_lookup        12.315  0.260  61.569
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking package vignettes ... NOTE
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 7 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/geneXtendeR.Rcheck/00check.log’
for details.


Installation output

geneXtendeR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL geneXtendeR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘geneXtendeR’ ...
** using staged installation
** libs
using C compiler: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c annotate.c -o annotate.o
annotate.c: In function 'annotate':
annotate.c:159:79: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
  159 |                 Rf_error("annotate() doesn't handle output lines longer than %d characters", sizeof(Buffer));
      |                                                                              ~^              ~~~~~~~~~~~~~~
      |                                                                               |              |
      |                                                                               int            long unsigned int
      |                                                                              %ld
annotate.c:191:87: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
  191 |                         Rf_error("annotate() doesn't handle output lines longer than %d characters",sizeof(Buffer));
      |                                                                                      ~^             ~~~~~~~~~~~~~~
      |                                                                                       |             |
      |                                                                                       int           long unsigned int
      |                                                                                      %ld
annotate.c:199:87: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
  199 |                         Rf_error("annotate() doesn't handle output lines longer than %d characters",sizeof(Buffer));
      |                                                                                      ~^             ~~~~~~~~~~~~~~
      |                                                                                       |             |
      |                                                                                       int           long unsigned int
      |                                                                                      %ld
annotate.c:208:87: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
  208 |                         Rf_error("annotate() doesn't handle output lines longer than %d characters",sizeof(Buffer));
      |                                                                                      ~^             ~~~~~~~~~~~~~~
      |                                                                                       |             |
      |                                                                                       int           long unsigned int
      |                                                                                      %ld
annotate.c:228:83: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
  228 |                     Rf_error("annotate() doesn't handle output lines longer than %d characters",sizeof(Buffer));
      |                                                                                  ~^             ~~~~~~~~~~~~~~
      |                                                                                   |             |
      |                                                                                   int           long unsigned int
      |                                                                                  %ld
gcc -I"/home/biocbuild/R/R-4.4.1/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;
      |            ^~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.4.1/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:202:79: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
  202 |                 Rf_error("annotate() doesn't handle output lines longer than %d characters", sizeof(Buffer));
      |                                                                              ~^              ~~~~~~~~~~~~~~
      |                                                                               |              |
      |                                                                               int            long unsigned int
      |                                                                              %ld
gcc -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o geneXtendeR.so annotate.o extract_number.o extract_peaks.o -L/home/biocbuild/R/R-4.4.1/lib -lR
installing to /home/biocbuild/R/R-4.4.1/site-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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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, aperm, 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, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    findMatches

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 
213.536   4.500 218.200 

Example timings

geneXtendeR.Rcheck/geneXtendeR-Ex.timings

nameusersystemelapsed
allPeakLengths0.0450.0000.050
annotate20.397 0.64532.090
annotate_n000
barChart20.086 0.63531.684
cumlinePlot19.759 0.43033.566
diffGO14.538 0.41426.662
distinct14.986 0.21627.705
gene_annotate16.688 0.22147.238
gene_lookup12.315 0.26061.569
hotspotPlot23.638 0.37043.665
linePlot19.558 0.34056.185
makeNetwork 15.119 0.619154.650
makeWordCloud 15.290 0.295233.850
meanPeakLength 13.354 0.236127.736
meanPeakLengthPlot44.195 0.66896.554
peakLengthBoxplot13.777 0.10429.491
peaksInput0.2610.0210.332
peaksMerge0.1560.0000.153
plotWordFreq14.304 0.25431.762
rat3.6770.1023.801
samplepeaksinput0.0090.0000.010