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###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2023.11.02/bin/R CMD check --install=check:EnrichmentBrowser.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library --no-vignettes --timings EnrichmentBrowser_2.33.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/EnrichmentBrowser.Rcheck’
* using R Under development (unstable) (2023-11-01 r85459)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    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 ‘EnrichmentBrowser/DESCRIPTION’ ... OK
* this is package ‘EnrichmentBrowser’ version ‘2.33.1’
* 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 ‘EnrichmentBrowser’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: 'pathview:::parseKGML2Graph2'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.getGOFromBiomart: no visible binding for global variable
  ‘go_linkage_type’
Undefined global functions or variables:
  go_linkage_type
* 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘EnrichmentBrowser-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ebrowser
> ### Title: Seamless navigation through enrichment analysis results
> ### Aliases: ebrowser
> 
> ### ** Examples
> 
> 
>     # expression data from file
>     exprs.file <- system.file("extdata/exprs.tab", package="EnrichmentBrowser")
>     cdat.file <- system.file("extdata/colData.tab", package="EnrichmentBrowser")
>     rdat.file <- system.file("extdata/rowData.tab", package="EnrichmentBrowser")
>     
>     # getting all human KEGG gene sets
>     # hsa.gs <- getGenesets(org="hsa", db="kegg")
>     gs.file <- system.file("extdata/hsa_kegg_gs.gmt", package="EnrichmentBrowser")
>     hsa.gs <- getGenesets(gs.file)
> 
>     # output destination 
>     out.dir <- configEBrowser("OUTDIR.DEFAULT") 
> 
>     # set-based enrichment analysis
>     ebrowser( meth="ora", perm=0,
+             exprs=exprs.file, cdat=cdat.file, rdat=rdat.file, 
+             gs=hsa.gs, org="hsa", nr.show=3,
+             out.dir=out.dir, report.name="oraReport")
Warning: Package 'ReportingTools' is deprecated and will be removed from
  Bioconductor version 3.19
Read expression data ...
Normalize ...
Excluding 211 genes not satisfying min.cpm threshold
Corresponding software package not found: EDASeq
Make sure that you have it installed.
Bioconductor version 3.19 (BiocManager 1.30.22), R Under development (unstable)
  (2023-11-01 r85459)
Installing package(s) 'BiocVersion', 'EDASeq'
also installing the dependencies 'deldir', 'RcppEigen', 'jpeg', 'interp', 'latticeExtra', 'ShortRead', 'aroma.light'

trying URL 'https://cloud.r-project.org/src/contrib/deldir_2.0-2.tar.gz'
Content type 'application/x-gzip' length 103483 bytes (101 KB)
==================================================
downloaded 101 KB

trying URL 'https://cloud.r-project.org/src/contrib/RcppEigen_0.3.3.9.4.tar.gz'
Content type 'application/x-gzip' length 1451521 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

trying URL 'https://cloud.r-project.org/src/contrib/jpeg_0.1-10.tar.gz'
Content type 'application/x-gzip' length 18667 bytes (18 KB)
==================================================
downloaded 18 KB

trying URL 'https://cloud.r-project.org/src/contrib/interp_1.1-4.tar.gz'
Content type 'application/x-gzip' length 1112571 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

trying URL 'https://cloud.r-project.org/src/contrib/latticeExtra_0.6-30.tar.gz'
Content type 'application/x-gzip' length 1292936 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/ShortRead_1.61.0.tar.gz'
Content type 'application/x-gzip' length 5233398 bytes (5.0 MB)
==================================================
downloaded 5.0 MB

trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/aroma.light_3.33.0.tar.gz'
Content type 'application/x-gzip' length 386662 bytes (377 KB)
==================================================
downloaded 377 KB

trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/BiocVersion_3.19.1.tar.gz'
Content type 'application/x-gzip' length 969 bytes
==================================================
downloaded 969 bytes

trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/EDASeq_2.37.0.tar.gz'
Content type 'application/x-gzip' length 1036738 bytes (1012 KB)
==================================================
downloaded 1012 KB

* installing *source* package ‘deldir’ ...
** package ‘deldir’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
using Fortran compiler: ‘GNU Fortran (GCC) 10.3.1’
gfortran  -fPIC  -g -O2  -Wall -c  acchk.f90 -o acchk.o
gfortran  -fPIC  -g -O2  -Wall -c  addpt.f90 -o addpt.o
gfortran  -fPIC  -g -O2  -Wall -c  adjchk.f90 -o adjchk.o
gfortran  -fPIC  -g -O2  -Wall -c  binsrt.f90 -o binsrt.o
gfortran  -fPIC  -g -O2  -Wall -c  circen.f90 -o circen.o
gfortran  -fPIC  -g -O2  -Wall -c  cross.f90 -o cross.o
cross.f90:101:23:

  101 | cprd = (a*d - b*c)/smin
      |                       ^
Warning: ‘smin’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gfortran  -fPIC  -g -O2  -Wall -c  delet.f90 -o delet.o
gfortran  -fPIC  -g -O2  -Wall -c  delet1.f90 -o delet1.o
gfortran  -fPIC  -g -O2  -Wall -c  delout.f90 -o delout.o
gfortran  -fPIC  -g -O2  -Wall -c  delseg.f90 -o delseg.o
gfortran  -fPIC  -g -O2  -Wall -c  dirout.f90 -o dirout.o
gfortran  -fPIC  -g -O2  -Wall -c  dirseg.f90 -o dirseg.o
gfortran  -fPIC  -g -O2  -Wall -c  dldins.f90 -o dldins.o
gcc -I"/home/biocbuild/R/R-devel/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c init.c -o init.o
gfortran  -fPIC  -g -O2  -Wall -c  initad.f90 -o initad.o
gfortran  -fPIC  -g -O2  -Wall -c  insrt.f90 -o insrt.o
gfortran  -fPIC  -g -O2  -Wall -c  insrt1.f90 -o insrt1.o
gfortran  -fPIC  -g -O2  -Wall -c  intri.f90 -o intri.o
gfortran  -fPIC  -g -O2  -Wall -c  locn.f90 -o locn.o
gfortran  -fPIC  -g -O2  -Wall -c  master.f90 -o master.o
gfortran  -fPIC  -g -O2  -Wall -c  mnnd.f90 -o mnnd.o
gfortran  -fPIC  -g -O2  -Wall -c  pred.f90 -o pred.o
gfortran  -fPIC  -g -O2  -Wall -c  qtest.f90 -o qtest.o
gfortran  -fPIC  -g -O2  -Wall -c  qtest1.f90 -o qtest1.o
gfortran  -fPIC  -g -O2  -Wall -c  stoke.f90 -o stoke.o
gfortran  -fPIC  -g -O2  -Wall -c  succ.f90 -o succ.o
gfortran  -fPIC  -g -O2  -Wall -c  swap.f90 -o swap.o
gfortran  -fPIC  -g -O2  -Wall -c  testeq.f90 -o testeq.o
gfortran  -fPIC  -g -O2  -Wall -c  triar.f90 -o triar.o
gfortran  -fPIC  -g -O2  -Wall -c  trifnd.f90 -o trifnd.o
gcc -shared -L/home/biocbuild/R/R-devel/lib -L/usr/local/lib -o deldir.so acchk.o addpt.o adjchk.o binsrt.o circen.o cross.o delet.o delet1.o delout.o delseg.o dirout.o dirseg.o dldins.o init.o initad.o insrt.o insrt1.o intri.o locn.o master.o mnnd.o pred.o qtest.o qtest1.o stoke.o succ.o swap.o testeq.o triar.o trifnd.o -lgfortran -lm -L/home/biocbuild/R/R-devel/lib -lR
installing to /home/biocbuild/tmp/RtmpiSvTlW/RLIBS_1119cd432ccc1f/00LOCK-deldir/00new/deldir/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (deldir)
* installing *source* package ‘RcppEigen’ ...
** package ‘RcppEigen’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-devel/include" -DNDEBUG  -I'/home/biocbuild/tmp/RtmpiSvTlW/RLIBS_1119cd432ccc1f/Rcpp/include' -I/usr/local/include   -I../inst/include -fPIC  -g -O2  -Wall -c RcppEigen.cpp -o RcppEigen.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-devel/include" -DNDEBUG  -I'/home/biocbuild/tmp/RtmpiSvTlW/RLIBS_1119cd432ccc1f/Rcpp/include' -I/usr/local/include   -I../inst/include -fPIC  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-devel/include" -DNDEBUG  -I'/home/biocbuild/tmp/RtmpiSvTlW/RLIBS_1119cd432ccc1f/Rcpp/include' -I/usr/local/include   -I../inst/include -fPIC  -g -O2  -Wall -c fastLm.cpp -o fastLm.o
g++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
make: *** [/home/biocbuild/R/R-devel/etc/Makeconf:200: fastLm.o] Error 1
ERROR: compilation failed for package ‘RcppEigen’
* removing ‘/home/biocbuild/tmp/RtmpiSvTlW/RLIBS_1119cd432ccc1f/RcppEigen’
installation of package 'RcppEigen' had non-zero exit status
* installing *source* package ‘jpeg’ ...
** package ‘jpeg’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-devel/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c read.c -o read.o
gcc -I"/home/biocbuild/R/R-devel/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c reg.c -o reg.o
gcc -I"/home/biocbuild/R/R-devel/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c write.c -o write.o
gcc -shared -L/home/biocbuild/R/R-devel/lib -L/usr/local/lib -o jpeg.so read.o reg.o write.o -ljpeg -L/home/biocbuild/R/R-devel/lib -lR
installing to /home/biocbuild/tmp/RtmpiSvTlW/RLIBS_1119cd432ccc1f/00LOCK-jpeg/00new/jpeg/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (jpeg)
* installing *source* package ‘aroma.light’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (aroma.light)
* installing *source* package ‘BiocVersion’ ...
** using staged installation
** help
*** installing help indices
** building package indices
** 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 (BiocVersion)
ERROR: dependency ‘RcppEigen’ is not available for package ‘interp’
* removing ‘/home/biocbuild/tmp/RtmpiSvTlW/RLIBS_1119cd432ccc1f/interp’
installation of package 'interp' had non-zero exit status
ERROR: dependency ‘interp’ is not available for package ‘latticeExtra’
* removing ‘/home/biocbuild/tmp/RtmpiSvTlW/RLIBS_1119cd432ccc1f/latticeExtra’
installation of package 'latticeExtra' had non-zero exit status
ERROR: dependency ‘latticeExtra’ is not available for package ‘ShortRead’
* removing ‘/home/biocbuild/tmp/RtmpiSvTlW/RLIBS_1119cd432ccc1f/ShortRead’
installation of package 'ShortRead' had non-zero exit status
ERROR: dependency ‘ShortRead’ is not available for package ‘EDASeq’
* removing ‘/home/biocbuild/tmp/RtmpiSvTlW/RLIBS_1119cd432ccc1f/EDASeq’
installation of package 'EDASeq' had non-zero exit status

The downloaded source packages are in
	'/home/biocbuild/tmp/RtmpxsRtzV/downloaded_packages'
Error in betweenLaneNormalization(assay(se), which = norm.method) : 
  could not find function "betweenLaneNormalization"
Calls: ebrowser -> normalize
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/EnrichmentBrowser.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2023.11.02/bin/R CMD INSTALL EnrichmentBrowser
###
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* installing to library ‘/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library’
* installing *source* package ‘EnrichmentBrowser’ ...
** using staged installation
** R
** 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 (EnrichmentBrowser)