Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-08-06 11:06:58 -0400 (Sat, 06 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4371
palomino4Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4155
lconwaymacOS 12.2.1 Montereyx86_644.2.1 Patched (2022-07-09 r82577) -- "Funny-Looking Kid" 4155
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

CHECK results for SMITE on palomino4


To the developers/maintainers of the SMITE package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SMITE.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1866/2137HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SMITE 1.25.0  (landing page)
Neil Ari Wijetunga
Snapshot Date: 2022-08-05 14:00:05 -0400 (Fri, 05 Aug 2022)
git_url: https://git.bioconductor.org/packages/SMITE
git_branch: master
git_last_commit: b145409
git_last_commit_date: 2022-04-26 11:29:16 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    NA  
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: SMITE
Version: 1.25.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SMITE.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings SMITE_1.25.0.tar.gz
StartedAt: 2022-08-06 06:06:50 -0400 (Sat, 06 Aug 2022)
EndedAt: 2022-08-06 06:11:26 -0400 (Sat, 06 Aug 2022)
EllapsedTime: 276.2 seconds
RetCode: 0
Status:   OK  
CheckDir: SMITE.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SMITE.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings SMITE_1.25.0.tar.gz
###
##############################################################################
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* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/SMITE.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'SMITE/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SMITE' version '1.25.0'
* 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 'SMITE' 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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... 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: OK


Installation output

SMITE.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/SMITE_1.25.0.tar.gz && rm -rf SMITE.buildbin-libdir && mkdir SMITE.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SMITE.buildbin-libdir SMITE_1.25.0.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL SMITE_1.25.0.zip && rm SMITE_1.25.0.tar.gz SMITE_1.25.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2790k  100 2790k    0     0  3935k      0 --:--:-- --:--:-- --:--:-- 3941k
only one architecture so ignoring '--merge-multiarch'
* installing *source* package 'SMITE' ...
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'SMITE' as SMITE_1.25.0.zip
* DONE (SMITE)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'SMITE' successfully unpacked and MD5 sums checked

Tests output


Example timings

SMITE.Rcheck/SMITE-Ex.timings

nameusersystemelapsed
Reactome.Symbol.Igraph0.130.030.16
SMITE-package0.310.030.34
addShadowText0.000.020.02
annotateExpression0.310.000.31
annotateModification000
convertGeneIds2.880.253.12
curated_expression0.030.010.05
extractExpression0.170.020.19
extractGOseq0.060.000.06
extractModification0.810.040.86
extractModules0.080.020.09
extractScores0.070.020.08
genes_for_conversiontest1.280.011.30
hg19_gene_bed0.170.000.17
highScores0.080.000.08
histone_h3k4me10.040.000.05
makePvalueAnnotation0.610.020.62
makePvalueObject0.050.010.06
methylationdata0.050.000.05
normalizePval0.060.000.06
plotCompareScores0.440.000.44
plotDensityPval0.090.000.09
plotModule0.060.020.08
removeModification0.10.00.1
runBioNet0.060.000.06
runGOseq0.060.000.07
runSpinglass0.530.020.54
scorePval0.070.020.08
stoufferTest0.010.000.02
test_annotation_score_data0.130.000.12