##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:metaseqR2.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings metaseqR2_1.4.14.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/metaseqR2.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metaseqR2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘metaseqR2’ version ‘1.4.14’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘metaseqR2’ 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 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 ‘metaseqR2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: metaseqr2
> ### Title: The main metaseqr2 pipeline
> ### Aliases: metaseqr2
> 
> ### ** Examples
> 
> # An example pipeline with gene counts
> data("mm9GeneData",package="metaseqR2")
> 
> result <- metaseqr2(
+     counts=mm9GeneCounts,
+     sampleList=sampleListMm9,
+     contrast=c("adult_8_weeks_vs_e14.5"),
+     libsizeList=libsizeListMm9,
+     annotation="embedded",
+     org="mm9",
+     countType="gene",
+     normalization="edger",
+     statistics="edger",
+     pcut=0.05,
+     figFormat="png",
+     qcPlots="mds",
+     exportWhat=c("annotation","p_value","adj_p_value","fold_change"),
+     exportScale="natural",
+     exportValues="normalized",
+     exportStats="mean",
+     exportWhere=file.path(tempdir(),"test1"),
+     restrictCores=0.1,
+     geneFilters=list(
+         length=list(
+             length=500
+         ),
+         avgReads=list(
+             averagePerBp=100,
+             quantile=0.25
+         ),
+         expression=list(
+             median=TRUE,
+             mean=FALSE,
+             quantile=NA,
+             known=NA,
+             custom=NA
+         ),
+         biotype=getDefaults("biotypeFilter","mm9")
+     ),
+     outList=TRUE
+ )
Warning: The column that contains the gene biotypes ("embedCols$btCol") is missing with embedded annotation! Biotype filters and certain plots will not be available...

2021-10-14 21:02:26: Data processing started...

Read counts file: imported custom data frame
Conditions: e14.5, adult_8_weeks
Samples to include: e14.5_1, e14.5_2, a8w_1, a8w_2
Samples to exclude: none
Requested contrasts: adult_8_weeks_vs_e14.5
Library sizes: 
  e14.5_1: 3102907
  e14.5_2: 2067905
  a8w_1: 3742059
  a8w_2: 4403954
Annotation: embedded
Organism: mm9
Reference source: ensembl
Count type: gene
Transcriptional level: gene
Exon filters: minActiveExons
  minActiveExons: 
    exonsPerGene: 5
    minExons: 2
    frac: 0.2
Gene filters: length, avgReads, expression
  length: 
    length: 500
  avgReads: 
    averagePerBp: 100
    quantile: 0.25
  expression: 
    median: TRUE
    mean: FALSE
    quantile: NA
    known: NA
    custom: NA
Filter application: postnorm
Normalization algorithm: edger
Normalization arguments: 
  method: TMM
  logratioTrim: 0.3
  sumTrim: 0.05
  doWeighting: TRUE
  Acutoff: -1e+10
  p: 0.75
Statistical algorithm(s): edger
Statistical arguments: 
  edger: classic, 5, 10, movingave, NULL, grid, 11, c(-6, 6), NULL, CoxReid, 10000, NULL, auto, NULL, NULL, NULL, NULL, 0.125, NULL, auto, chisq, TRUE, FALSE, c(0.05, 0.1)
Meta-analysis method: none
Multiple testing correction: BH
p-value threshold: 0.05
Logarithmic transformation offset: 1
Quality control plots: mds
Figure format: png
Output directory: /tmp/RtmpIW4dvj/test1
Output data: annotation, p_value, adj_p_value, fold_change
Output scale(s): natural
Output values: normalized
Loading gene annotation...
Saving gene model to /tmp/RtmpIW4dvj/test1/data/gene_model.RData
Removing genes with zero counts in all samples...
Normalizing with: edger
Applying gene filter length...
  Threshold below which ignored: 500
Applying gene filter avgReads...
  Threshold below which ignored: 0.0659629215631332
Applying gene filter expression...
  Threshold below which ignored: 68
2106 genes filtered out
1681 genes remain after filtering
Running statistical tests with: edger
  Contrast: adult_8_weeks_vs_e14.5
  Contrast adult_8_weeks_vs_e14.5: found 906 genesError in .check_ncores(cores) : 3 simultaneous processes spawned
Calls: metaseqr2 -> cmclapply -> mclapply -> .check_ncores
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* 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
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/metaseqR2.Rcheck/00check.log’
for details.