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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:LowMACA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings LowMACA_1.31.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/LowMACA.Rcheck’
* using R version 4.3.1 Patched (2023-06-17 r84564)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.5
* 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 for sufficient/correct file permissions ... 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: alignSequences
> ### Title: Align sequences via clustalo
> ### Aliases: alignSequences
> 
> ### ** Examples
> 
> #Create an object of class LowMACA for RAS domain family
> lm <- newLowMACA(pfam="PF00071" , genes=c("KRAS" , "NRAS" , "HRAS"))
All Gene Symbols correct!
> #Align sequences using local installation of clustalo
> lm <- alignSequences(lm)
Aligning sequences...
> #Web service clustalomega aligner
> lm <- alignSequences(lm , mail="lowmaca@gmail.com")
Aligning sequences...
Checking perl installation...
Checking perl modules XML::Simple and LWP...
JobId: clustalo-R20230701-014923-0951-50358133-p1m
QUEUED
http status: 400 Bad Request  Job 'clustalo-R20230701-014923-0951-50358133-p1m' is still queued at /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/LowMACA/clustalo_lwp.pl line 262.
Warning in system(exec, intern = TRUE) :
  running command ''/usr/bin/perl' '/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/LowMACA/clustalo_lwp.pl' --noguidetreeout --stype protein --dismatout --outfmt clustal --email lowmaca@gmail.com --outfile '/tmp/RtmpmamTPG/webClustal' '/tmp/RtmpmamTPG/file66f574b855d6'' had status 255
Error in .clustalOAlign(genesData, clustal_cmd, clustalo_filename, mail,  : 
  Alignment with ClustalOmega had non 0 exit status:
Calls: 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
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/LowMACA.Rcheck/00check.log’
for details.

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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL LowMACA
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/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)