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### Running command:
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###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:rgsepd.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings rgsepd_1.34.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/rgsepd.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 ‘rgsepd/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rgsepd’ version ‘1.34.0’
* 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 ‘rgsepd’ 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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    Rebuilt for R 3.2.2
* 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 startup messages can be suppressed ... NOTE
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘rgsepd-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ExtractProjection
> ### Title: ExtractProjection
> ### Aliases: ExtractProjection
> ### Keywords: plot
> 
> ### ** Examples
> 
> 
>   data("IlluminaBodymap")
>   data("IlluminaBodymapMeta")
>   set.seed(1000) #fixed randomness
>   x <- Name_to_RefSeq(c("HIF1A","EGFR","MYH7","CD33","BRCA2"))
>   isoform_ids = intersect(x, rownames(IlluminaBodymap))
>   rows_of_interest <- unique( c( isoform_ids ,
+                                  sample(rownames(IlluminaBodymap),
+                                         size=2000,replace=FALSE)))
>   G <- GSEPD_INIT(Output_Folder="OUT",
+                 finalCounts=round(IlluminaBodymap[rows_of_interest , ]),
+                 sampleMeta=IlluminaBodymapMeta,
+                 COLORS=c("green","black","red"))
Keeping rows with counts (1821 of 2003)
>                 
>   G <- GSEPD_ChangeConditions( G, c("A","B")) #set testing groups first!    
>   G <- GSEPD_Process( G ) #have to have processed results to plot them
converting counts to integer mode
Generating OUT/DESEQ.counts.Ax4.Bx8.csv
converting counts to integer mode
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
using 'normal' for LFC shrinkage, the Normal prior from Love et al (2014).

Note that type='apeglm' and type='ashr' have shown to have less bias than type='normal'.
See ?lfcShrink for more details on shrinkage type, and the DESeq2 vignette.
Reference: https://doi.org/10.1093/bioinformatics/bty895
Generating OUT/DESEQ.Volcano.Ax4.Bx8.png
Generating OUT/DESEQ.RES.Ax4.Bx8.csv
dropping rows with raw PVAL>0.990 OR baseMean < 1 OR on excludes list
deseq txid rows remaining: 868
Converting identifiers with local DB
Generating OUT/DESEQ.RES.Ax4.Bx8.Annote.csv
Generating OUT/HM.Ax4.Bx8.330.pdf
Loading hg19 length data...
Fetching GO annotations...
Loading required package: AnnotationDbi
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns
Loading hg19 length data...
Fetching GO annotations...
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns
Loading hg19 length data...
Fetching GO annotations...
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
Generating OUT/GOSEQ.RES.Ax4.Bx8.GO.csv
Written GO categories, now reverse mapping
* 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-3.18-bioc/meat/rgsepd.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL rgsepd
###
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* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘rgsepd’ ...
** using staged installation
** 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
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
** testing if installed package can be loaded from final location
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
** testing if installed package keeps a record of temporary installation path
* DONE (rgsepd)