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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:IsoformSwitchAnalyzeR.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings IsoformSwitchAnalyzeR_2.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/IsoformSwitchAnalyzeR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* 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 ‘IsoformSwitchAnalyzeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IsoformSwitchAnalyzeR’ version ‘2.2.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'limma', 'DEXSeq', 'satuRn', 'sva', 'ggplot2', 'pfamAnalyzeR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘IsoformSwitchAnalyzeR’ can be installed ... OK
* used C compiler: ‘gcc (GCC) 10.3.1’
* checking installed package size ... NOTE
  installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data      1.1Mb
    extdata   4.4Mb
* 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘IsoformSwitchAnalyzeR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: importSalmonData
> ### Title: Direct creation of a switchAnalyzeRlist from Salmon
> ###   quantification
> ### Aliases: importSalmonData
> 
> ### ** Examples
> 
> ### Please note
> # The way of importing files in the following example with
> #   "system.file('pathToFile', package="IsoformSwitchAnalyzeR") is
> #   specialized way of accessing the example data in the IsoformSwitchAnalyzeR package
> #   and not something you need to do - just supply the string e.g.
> #   parentDir = "individual_quantifications_in_subdir/" to the functions
> #   path (e.g. "myAnnotation/isoformsQuantified.gtf") to the isoformExonAnnoation argument
> 
> ### Prepare data.frame with quant file info
> salmonDf <- prepareSalmonFileDataFrame(
+     system.file("extdata/drosophila", package="IsoformSwitchAnalyzeR")
+ )
Found 4 Salmon quantifications of interest
Adding NAs as conditions. Please modify these manually.
> 
> ### Add conditions
> salmonDf$condition <- c('wt','wt','ko','ko')
> 
> ### Create switchAnalyzeRlist
> aSwitchList <- importSalmonData(salmonDf)
Importing quantification data...
Importing annoation data...
trying URL 'ftp://ftp.ensembl.org/pub/release-98/fasta/drosophila_melanogaster/cdna/Drosophila_melanogaster.BDGP6.22.cdna.all.fa.gz'
Content type 'unknown' length 17378397 bytes (16.6 MB)
==================================================
Warning: call dbDisconnect() when finished working with a connection
trying URL 'ftp://ftp.ensembl.org/pub/release-98/fasta/drosophila_melanogaster/ncrna/Drosophila_melanogaster.BDGP6.22.ncrna.fa.gz'
Content type 'unknown' length 956972 bytes (934 KB)
==================================================
Massaging data...
Making switchAnalyzeRlist...
Step 1 of 10: Checking data...
Step 2 of 10: Obtaining annotation...
    importing GTF (this may take a while)...
trying URL 'ftp://ftp.ensembl.org/pub/release-98/gtf/drosophila_melanogaster/Drosophila_melanogaster.BDGP6.22.98.gtf.gz'
Content type 'unknown' length 5896048 bytes (5.6 MB)
==================================================
* 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, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/IsoformSwitchAnalyzeR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL IsoformSwitchAnalyzeR
###
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* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘IsoformSwitchAnalyzeR’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c utils.c -o utils.o
gcc -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/lib -o IsoformSwitchAnalyzeR.so utils.o -L/home/biocbuild/R/R-4.3.1/lib -lR
installing to /home/biocbuild/R/R-4.3.1/site-library/00LOCK-IsoformSwitchAnalyzeR/00new/IsoformSwitchAnalyzeR/libs
** R
** data
** 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 (IsoformSwitchAnalyzeR)