Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:06:24 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
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 |
To the developers/maintainers of the SANTA package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SANTA.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. |
Package 1766/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SANTA 2.34.0 (landing page) Alex Cornish
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
Package: SANTA |
Version: 2.34.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SANTA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SANTA_2.34.0.tar.gz |
StartedAt: 2023-04-10 22:26:08 -0400 (Mon, 10 Apr 2023) |
EndedAt: 2023-04-10 22:27:09 -0400 (Mon, 10 Apr 2023) |
EllapsedTime: 60.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SANTA.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SANTA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SANTA_2.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/SANTA.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SANTA/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SANTA’ version ‘2.34.0’ * 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 ‘SANTA’ 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 ... OK * 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 NOTE See ‘/Users/biocbuild/bbs-3.16-bioc/meat/SANTA.Rcheck/00check.log’ for details.
SANTA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SANTA ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’ * installing *source* package ‘SANTA’ ... ** using staged installation ** libs clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c computenetK_fewzeros.c -o computenetK_fewzeros.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c computenodeAUK.c -o computenodeAUK.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c computeweights.c -o computeweights.o clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o SANTA.so computenetK_fewzeros.o computenodeAUK.o computeweights.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-SANTA/00new/SANTA/libs ** 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 absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (SANTA)
SANTA.Rcheck/tests/runTests.Rout
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > BiocGenerics:::testPackage("SANTA") Attaching package: 'igraph' The following objects are masked from 'package:stats': decompose, spectrum The following object is masked from 'package:base': union computing graph distance bins... done computing graph distance bins... done computing graph distance bins... done computing graph distance bins... done computing graph distance bins... done computing graph distance bins... done computing graph distance bins... done computing graph distance bins... done computing graph distance bins... done computing graph distance bins... done computing graph distance bins... done computing graph distance bins... computing graph distance bins... computing graph distance bins... done no edge attribute with name 'distance' found so all edge distances set to 1 computing graph distance matrix... done no edge attribute with name 'distance' found so all edge distances set to 1 computing graph distance matrix... done computing graph distance matrix... done computing graph distance matrix... done computing graph distance matrix... done computing graph distance matrix... done computing graph distance matrix... done computing graph distance matrix... done computing graph distance matrix... done computing graph distance matrix... done computing graph distance matrix... done Warning: stack imbalance in '<-', 25 then 26 Warning: stack imbalance in '<-', 26 then 27 Warning: stack imbalance in '{', 21 then 23 computing graph distance matrix... done computing graph distance matrix... done computing graph distance matrix... done computing graph distance matrix... done computing graph distance matrix... done computing graph distance matrix... done computing graph distance matrix... done computing graph distance matrix... done computing graph distance matrix... done computing graph distance matrix... done computing graph distance matrix... done computing graph distance matrix... done computing graph distance matrix... done computing graph distance matrix... done computing graph distance matrix... done computing graph distance matrix... done RUNIT TEST PROTOCOL -- Mon Apr 10 22:26:59 2023 *********************************************** Number of test functions: 13 Number of errors: 0 Number of failures: 0 1 Test Suite : SANTA RUnit Tests - 13 test functions, 0 errors, 0 failures Number of test functions: 13 Number of errors: 0 Number of failures: 0 Warning messages: 1: In SANTA:::CheckAttributes(g, vertex.attr = "vertex.attr") : non-numeric/non-logical vertex weights found and converted to numerals 2: In SANTA:::CheckAttributes(g, vertex.attr = "vertex.attr") : NAs introduced by coercion 3: In SpreadHits(g, h = 2, clusters = 3, distance.cutoff = 20, lambda = 10, : seed vertices not identified > > proc.time() user system elapsed 6.285 1.656 7.950
SANTA.Rcheck/SANTA-Ex.timings
name | user | system | elapsed | |
BinGraph | 0.101 | 0.011 | 0.112 | |
CreateGrid | 0.020 | 0.001 | 0.022 | |
DistGraph | 0.017 | 0.003 | 0.021 | |
GraphDiffusion | 0.007 | 0.001 | 0.010 | |
GraphMFPT | 0.028 | 0.005 | 0.034 | |
Knet | 0.030 | 0.006 | 0.036 | |
Knode | 0.026 | 0.003 | 0.030 | |
SANTA.data | 0.012 | 0.004 | 0.015 | |
SpreadHits | 0.016 | 0.001 | 0.017 | |
plot.Knet | 0.025 | 0.004 | 0.028 | |