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This page was generated on 2023-10-16 11:36:17 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1081/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LowMACA 1.30.0  (landing page)
Giorgio Melloni , Stefano de Pretis
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/LowMACA
git_branch: RELEASE_3_17
git_last_commit: 0eaae9e
git_last_commit_date: 2023-04-25 10:38:36 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    ERROR  skipped
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for LowMACA on palomino3


To the developers/maintainers of the LowMACA package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/LowMACA.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: LowMACA
Version: 1.30.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:LowMACA.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings LowMACA_1.30.0.tar.gz
StartedAt: 2023-10-16 03:33:31 -0400 (Mon, 16 Oct 2023)
EndedAt: 2023-10-16 03:44:50 -0400 (Mon, 16 Oct 2023)
EllapsedTime: 679.0 seconds
RetCode: 0
Status:   OK  
CheckDir: LowMACA.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:LowMACA.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings LowMACA_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-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 '1.30.0'
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
allPfamAnalysis   109.64   2.64  124.61
lfmSingleSequence  59.62   1.46   67.26
setup              23.53   0.50   45.61
LowMACA-class      16.62   0.56   32.08
LowMACA-package    10.33   0.29   14.67
getMutations        3.02   0.10    5.42
alignSequences      1.97   0.15   23.34
* 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 NOTE
See
  'F:/biocbuild/bbs-3.17-bioc/meat/LowMACA.Rcheck/00check.log'
for details.



Installation output

LowMACA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL LowMACA
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-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)

Tests output


Example timings

LowMACA.Rcheck/LowMACA-Ex.timings

nameusersystemelapsed
BLOSUM62000
LowMACA-class16.62 0.5632.08
LowMACA-package10.33 0.2914.67
LowMACA_AML0.030.000.04
alignSequences 1.97 0.1523.34
allPfamAnalysis109.64 2.64124.61
bpAll0.780.010.80
entropy0.730.000.73
getMutations3.020.105.42
lfm1.330.041.38
lfmSingleSequence59.62 1.4667.26
lmAlignment0.050.000.05
lmEntropy0.670.040.72
lmMutations0.030.000.03
lmObj0.080.000.08
lmParams0.420.020.89
lmPlot2.380.042.42
lmPlotSingleSequence3.010.023.48
mapMutations0.470.000.47
newLowMACA2.360.022.38
nullProfile0.720.030.75
parallelize0.390.000.39
protter0.690.042.33
setup23.53 0.5045.61
showTumorType0.180.000.47