##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:geneXtendeR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings geneXtendeR_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/geneXtendeR.Rcheck'
* using R version 4.4.3 (2025-02-28 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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 long unsigned int' [-Wformat=]
  annotate.c:191:87: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
  annotate.c:199:87: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
  annotate.c:208:87: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
  annotate.c:228:83: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
  extract_peaks.c:202:79: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
See 'F:/biocbuild/bbs-3.20-bioc/meat/geneXtendeR.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.3.0'
* checking installed package size ... NOTE
  installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data      5.7Mb
    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 5.7 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 for x64 is not available
File 'F:/biocbuild/bbs-3.20-bioc/R/library/geneXtendeR/libs/x64/geneXtendeR.dll':
  Found '_exit', possibly from '_exit' (C)
  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 nor [v]sprintf. 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 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 67.03   2.36   71.39
hotspotPlot        53.90   1.27   57.17
linePlot           40.30   0.62   42.91
cumlinePlot        37.97   0.79   40.71
barChart           35.18   0.65   37.80
annotate           31.68   0.38   34.00
gene_annotate      29.91   0.44   32.33
makeWordCloud      29.42   0.53   31.92
plotWordFreq       29.01   0.60   31.60
distinct           29.05   0.44   31.42
makeNetwork        28.84   0.61   31.59
peakLengthBoxplot  27.47   0.39   30.01
diffGO             27.02   0.62   30.89
gene_lookup        26.47   0.29   28.78
meanPeakLength     25.58   0.39   27.91
rat                 5.64   0.34    5.98
* 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
  'F:/biocbuild/bbs-3.20-bioc/meat/geneXtendeR.Rcheck/00check.log'
for details.

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL geneXtendeR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'geneXtendeR' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.3.0'
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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 long unsigned int' [-Wformat=]
  159 |                 Rf_error("annotate() doesn't handle output lines longer than %d characters", sizeof(Buffer));
      |                                                                              ~^              ~~~~~~~~~~~~~~
      |                                                                               |              |
      |                                                                               int            long long unsigned int
      |                                                                              %lld
annotate.c:191:87: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
  191 |                         Rf_error("annotate() doesn't handle output lines longer than %d characters",sizeof(Buffer));
      |                                                                                      ~^             ~~~~~~~~~~~~~~
      |                                                                                       |             |
      |                                                                                       int           long long unsigned int
      |                                                                                      %lld
annotate.c:199:87: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
  199 |                         Rf_error("annotate() doesn't handle output lines longer than %d characters",sizeof(Buffer));
      |                                                                                      ~^             ~~~~~~~~~~~~~~
      |                                                                                       |             |
      |                                                                                       int           long long unsigned int
      |                                                                                      %lld
annotate.c:208:87: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
  208 |                         Rf_error("annotate() doesn't handle output lines longer than %d characters",sizeof(Buffer));
      |                                                                                      ~^             ~~~~~~~~~~~~~~
      |                                                                                       |             |
      |                                                                                       int           long long unsigned int
      |                                                                                      %lld
annotate.c:228:83: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long long unsigned int' [-Wformat=]
  228 |                     Rf_error("annotate() doesn't handle output lines longer than %d characters",sizeof(Buffer));
      |                                                                                  ~^             ~~~~~~~~~~~~~~
      |                                                                                   |             |
      |                                                                                   int           long long unsigned int
      |                                                                                  %lld
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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 long unsigned int' [-Wformat=]
  202 |                 Rf_error("annotate() doesn't handle output lines longer than %d characters", sizeof(Buffer));
      |                                                                              ~^              ~~~~~~~~~~~~~~
      |                                                                               |              |
      |                                                                               int            long long unsigned int
      |                                                                              %lld
gcc -shared -s -static-libgcc -o geneXtendeR.dll tmp.def annotate.o extract_number.o extract_peaks.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.20-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
** 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)

R version 4.4.3 (2025-02-28 ucrt) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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

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 
 237.56   16.50  255.76