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###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:LowMACA.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings LowMACA_1.31.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/LowMACA.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'LowMACA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'LowMACA' version '1.31.0'
* 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 whether package 'LowMACA' 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 startup messages can be suppressed ... NOTE
Checking if clustalo is in the PATH...
Checking clustalo Version...
Checking perl installation...
Checking perl modules XML::Simple and LWP...

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 'LowMACA-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: setup
> ### Title: Setup of a LowMACA object
> ### Aliases: setup
> 
> ### ** Examples
> 
> #Create an object of class LowMACA for RAS domain family
> lm <- newLowMACA(pfam="PF00071" , genes=c("KRAS" , "NRAS" , "HRAS"))
All Gene Symbols correct!
> #Select a few tumor types
> lmParams(lm)$tumor_type <- c("skcm" , "brca" , "coadread")
> #Align sequences, get mutation data and map them on consensus
> lm <- setup(lm)
Aligning sequences...
Getting mutations from cancers studies...
ProfileId brca_mbcproject_wagle_2017 has no samples with mutations
> #Same as above, but using web service
> lm <- setup(lm , mail="lowmaca@gmail.com")
Aligning sequences...
Checking perl installation...
Checking perl modules XML::Simple and LWP...
JobId: clustalo-R20230701-074631-0305-28216410-p1m
QUEUED
http status: 400 Bad Request  Job 'clustalo-R20230701-074631-0305-28216410-p1m' is still queued at F:/biocbuild/bbs-3.18-bioc/R/library/LowMACA/clustalo_lwp.pl line 262.
Warning in system(exec, intern = TRUE) :
  running command '"C:\STRAWB~1\perl\bin\perl.exe" "F:/biocbuild/bbs-3.18-bioc/R/library/LowMACA/clustalo_lwp.pl" --noguidetreeout --stype protein --dismatout --outfmt clustal --email lowmaca@gmail.com --outfile "F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpqY5tAh/webClustal" "F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpqY5tAh\file27f862b41c6"' had status 9
Error in .clustalOAlign(genesData, clustal_cmd, clustalo_filename, mail,  : 
  Alignment with ClustalOmega had non 0 exit status:
Calls: setup ... setup -> alignSequences -> alignSequences -> .clustalOAlign
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, 1 NOTE
See
  'F:/biocbuild/bbs-3.18-bioc/meat/LowMACA.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL LowMACA
###
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* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library'
* installing *source* package 'LowMACA' ...
** 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
Checking if clustalo is in the PATH...
Checking clustalo Version...
Checking perl installation...
Checking perl modules XML::Simple and LWP...
** testing if installed package can be loaded from final location
Checking if clustalo is in the PATH...
Checking clustalo Version...
Checking perl installation...
Checking perl modules XML::Simple and LWP...
** testing if installed package keeps a record of temporary installation path
* DONE (LowMACA)