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This page was generated on 2024-05-20 11:32:12 -0400 (Mon, 20 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4381
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Package 792/2233HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
geneXtendeR 1.31.0  (landing page)
Bohdan Khomtchouk
Snapshot Date: 2024-05-18 09:00:01 -0400 (Sat, 18 May 2024)
git_url: https://git.bioconductor.org/packages/geneXtendeR
git_branch: devel
git_last_commit: 0558d4d
git_last_commit_date: 2024-04-30 10:54:08 -0400 (Tue, 30 Apr 2024)
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for geneXtendeR on kjohnson1


To the developers/maintainers of the geneXtendeR package:
- 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.

raw results


Summary

Package: geneXtendeR
Version: 1.31.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:geneXtendeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings geneXtendeR_1.31.0.tar.gz
StartedAt: 2024-05-19 14:10:16 -0400 (Sun, 19 May 2024)
EndedAt: 2024-05-19 14:23:30 -0400 (Sun, 19 May 2024)
EllapsedTime: 794.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: geneXtendeR.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:geneXtendeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings geneXtendeR_1.31.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/geneXtendeR.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘geneXtendeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘geneXtendeR’ version ‘1.31.0’
* 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:159:94: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  annotate.c:191:101: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  annotate.c:199:101: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  annotate.c:208:101: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  annotate.c:228:97: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
  extract_peaks.c:202:94: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
See ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/geneXtendeR.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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 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 sizes of PDF files under ‘inst/doc’ ... OK
* 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 35.461  3.326  40.277
hotspotPlot        24.740  0.994  26.191
annotate           22.584  0.399  23.778
linePlot           20.137  0.629  21.348
barChart           19.863  0.641  21.194
cumlinePlot        18.976  0.554  20.412
gene_annotate      18.035  0.419  18.868
diffGO             17.279  0.678  18.705
makeNetwork        15.870  0.546  16.910
makeWordCloud      15.036  0.613  16.136
distinct           14.514  0.344  15.479
peakLengthBoxplot  13.948  0.483  16.436
meanPeakLength     13.800  0.506  14.794
plotWordFreq       13.270  0.531  14.243
gene_lookup        13.236  0.259  13.912
* 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
  ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/geneXtendeR.Rcheck/00check.log’
for details.


Installation output

geneXtendeR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL geneXtendeR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘geneXtendeR’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c annotate.c -o annotate.o
annotate.c:159:94: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
                Rf_error("annotate() doesn't handle output lines longer than %d characters", sizeof(Buffer));
                                                                             ~~              ^~~~~~~~~~~~~~
                                                                             %lu
annotate.c:191:101: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
                        Rf_error("annotate() doesn't handle output lines longer than %d characters",sizeof(Buffer));
                                                                                     ~~             ^~~~~~~~~~~~~~
                                                                                     %lu
annotate.c:199:101: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
                        Rf_error("annotate() doesn't handle output lines longer than %d characters",sizeof(Buffer));
                                                                                     ~~             ^~~~~~~~~~~~~~
                                                                                     %lu
annotate.c:208:101: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
                        Rf_error("annotate() doesn't handle output lines longer than %d characters",sizeof(Buffer));
                                                                                     ~~             ^~~~~~~~~~~~~~
                                                                                     %lu
annotate.c:228:97: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
                    Rf_error("annotate() doesn't handle output lines longer than %d characters",sizeof(Buffer));
                                                                                 ~~             ^~~~~~~~~~~~~~
                                                                                 %lu
5 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c extract_number.c -o extract_number.o
extract_number.c:50:12: warning: variable 'pvcfcol1_1' set but not used [-Wunused-but-set-variable]
    char * pvcfcol1_1;
           ^
extract_number.c:51:12: warning: variable 'pvcfcol2_2' set but not used [-Wunused-but-set-variable]
    char * pvcfcol2_2;
           ^
extract_number.c:52:12: warning: variable 'pvcfcol3_3' set but not used [-Wunused-but-set-variable]
    char * pvcfcol3_3;
           ^
extract_number.c:53:12: warning: variable 'pvcfcol4_4' set but not used [-Wunused-but-set-variable]
    char * pvcfcol4_4;
           ^
extract_number.c:54:12: warning: variable 'pvcfcol5_5' set but not used [-Wunused-but-set-variable]
    char * pvcfcol5_5;
           ^
extract_number.c:66:10: warning: variable 'j_1' set but not used [-Wunused-but-set-variable]
    long j_1;
         ^
extract_number.c:72:10: warning: variable 'n_1' set but not used [-Wunused-but-set-variable]
    long n_1;
         ^
7 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c extract_peaks.c -o extract_peaks.o
extract_peaks.c:202:94: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
                Rf_error("annotate() doesn't handle output lines longer than %d characters", sizeof(Buffer));
                                                                             ~~              ^~~~~~~~~~~~~~
                                                                             %lu
1 warning generated.
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o geneXtendeR.so annotate.o extract_number.o extract_peaks.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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, 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 
169.220  14.704 185.614 

Example timings

geneXtendeR.Rcheck/geneXtendeR-Ex.timings

nameusersystemelapsed
allPeakLengths0.0440.0060.054
annotate22.584 0.39923.778
annotate_n000
barChart19.863 0.64121.194
cumlinePlot18.976 0.55420.412
diffGO17.279 0.67818.705
distinct14.514 0.34415.479
gene_annotate18.035 0.41918.868
gene_lookup13.236 0.25913.912
hotspotPlot24.740 0.99426.191
linePlot20.137 0.62921.348
makeNetwork15.870 0.54616.910
makeWordCloud15.036 0.61316.136
meanPeakLength13.800 0.50614.794
meanPeakLengthPlot35.461 3.32640.277
peakLengthBoxplot13.948 0.48316.436
peaksInput0.1060.0320.158
peaksMerge0.0500.0050.057
plotWordFreq13.270 0.53114.243
rat3.2990.3073.647
samplepeaksinput0.0100.0010.011