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This page was generated on 2022-01-21 11:07:36 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4163
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4058
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4000
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4117
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 riesling1


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? here 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 737/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
geneXtendeR 1.21.0  (landing page)
Bohdan Khomtchouk
Snapshot Date: 2022-01-20 13:55:17 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/geneXtendeR
git_branch: master
git_last_commit: 63b6b7a
git_last_commit_date: 2021-10-26 12:30:30 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  NO, package depends on 'rtracklayer' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: geneXtendeR
Version: 1.21.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:geneXtendeR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings geneXtendeR_1.21.0.tar.gz
StartedAt: 2022-01-20 18:57:54 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 19:11:42 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 827.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: geneXtendeR.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:geneXtendeR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings geneXtendeR_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/geneXtendeR.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'geneXtendeR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'geneXtendeR' version '1.21.0'
* 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 whether package 'geneXtendeR' can be installed ... OK
* 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 LazyData ... WARNING
  LazyData DB of 5.8 MB without LazyDataCompression set
  See ยง1.1.6 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 for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/geneXtendeR/libs/x64/geneXtendeR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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 46.33   2.11   56.98
hotspotPlot        28.88   1.97   39.00
barChart           27.77   1.11   35.93
linePlot           24.26   1.36   31.33
cumlinePlot        23.10   1.38   28.91
annotate           22.84   0.56   33.27
makeWordCloud      20.77   0.89   35.17
diffGO             18.47   1.08   24.74
meanPeakLength     18.48   0.72   26.22
distinct           16.58   0.76   21.42
gene_annotate      16.56   0.74   21.86
peakLengthBoxplot  15.72   0.50   21.49
plotWordFreq       14.75   0.61   20.72
gene_lookup        13.97   0.70   19.20
makeNetwork        13.83   0.72   19.50
* 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
  'D:/biocbuild/bbs-3.15-bioc/meat/geneXtendeR.Rcheck/00check.log'
for details.



Installation output

geneXtendeR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL geneXtendeR
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'geneXtendeR' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c annotate.c -o annotate.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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;
            ^~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c extract_peaks.c -o extract_peaks.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o geneXtendeR.dll tmp.def annotate.o extract_number.o extract_peaks.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-geneXtendeR/00new/geneXtendeR/libs/x64
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'geneXtendeR'
    finding HTML links ... done
    allPeakLengths                          html  
    annotate                                html  
    annotate_n                              html  
    barChart                                html  
    cumlinePlot                             html  
    diffGO                                  html  
    distinct                                html  
    dot-geneXtender                         html  
    gene_annotate                           html  
    gene_lookup                             html  
    hotspotPlot                             html  
    linePlot                                html  
    makeNetwork                             html  
    makeWordCloud                           html  
    meanPeakLength                          html  
    meanPeakLengthPlot                      html  
    peakLengthBoxplot                       html  
    peaksInput                              html  
    peaksMerge                              html  
    plotWordFreq                            html  
    rat                                     html  
    samplepeaksinput                        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (geneXtendeR)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'QuasR' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'VCFArray' is missing or broken
 done

Tests output

geneXtendeR.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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

Attaching package: 'IRanges'

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

    windows

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 
 149.79   16.56  167.76 

Example timings

geneXtendeR.Rcheck/geneXtendeR-Ex.timings

nameusersystemelapsed
allPeakLengths0.120.010.14
annotate22.84 0.5633.27
annotate_n000
barChart27.77 1.1135.93
cumlinePlot23.10 1.3828.91
diffGO18.47 1.0824.74
distinct16.58 0.7621.42
gene_annotate16.56 0.7421.86
gene_lookup13.97 0.7019.20
hotspotPlot28.88 1.9739.00
linePlot24.26 1.3631.33
makeNetwork13.83 0.7219.50
makeWordCloud20.77 0.8935.17
meanPeakLength18.48 0.7226.22
meanPeakLengthPlot46.33 2.1156.98
peakLengthBoxplot15.72 0.5021.49
peaksInput1.010.071.14
peaksMerge0.270.000.26
plotWordFreq14.75 0.6120.72
rat3.870.524.39
samplepeaksinput000