##############################################################################
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###
### 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_1.32.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/geneXtendeR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘geneXtendeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘geneXtendeR’ version ‘1.32.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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/meat/geneXtendeR.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* 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 28.417  2.161  32.809
hotspotPlot        16.170  0.821  19.108
linePlot           13.077  0.490  15.628
barChart           12.502  0.509  15.321
annotate           12.404  0.285  14.755
cumlinePlot        12.149  0.410  20.836
gene_annotate      11.186  0.370  13.573
makeNetwork        10.595  0.458  13.172
makeWordCloud      10.328  0.522  12.869
plotWordFreq        9.877  0.512  12.408
diffGO              9.372  0.430  11.799
distinct            9.514  0.277  11.767
meanPeakLength      9.386  0.339  11.732
peakLengthBoxplot   9.194  0.302  11.493
gene_lookup         8.481  0.210  10.683
* 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/meat/geneXtendeR.Rcheck/00check.log’
for details.

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘geneXtendeR’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c extract_number.c -o extract_number.o
extract_number.c:66:10: warning: variable 'j_1' set but not used [-Wunused-but-set-variable]
    long j_1;
         ^
extract_number.c:51:12: warning: variable 'pvcfcol2_2' set but not used [-Wunused-but-set-variable]
    char * pvcfcol2_2;
           ^
extract_number.c:72:10: warning: variable 'n_1' set but not used [-Wunused-but-set-variable]
    long n_1;
         ^
extract_number.c:50:12: warning: variable 'pvcfcol1_1' set but not used [-Wunused-but-set-variable]
    char * pvcfcol1_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;
           ^
7 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/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 x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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-x86_64/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)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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, 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 
115.857  14.366 131.067