Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:37 -0000 (Wed, 01 Mar 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
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To the developers/maintainers of the BUS package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BUS.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 234/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BUS 1.55.0 (landing page) Yuanhua Liu
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
Package: BUS |
Version: 1.55.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:BUS.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings BUS_1.55.0.tar.gz |
StartedAt: 2023-02-27 22:27:09 -0000 (Mon, 27 Feb 2023) |
EndedAt: 2023-02-27 22:27:44 -0000 (Mon, 27 Feb 2023) |
EllapsedTime: 35.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BUS.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:BUS.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings BUS_1.55.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/BUS.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘BUS/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BUS’ version ‘1.55.0’ * 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 ‘BUS’ can be installed ... OK * used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ * 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 ... NOTE Package in Depends field not imported from: ‘minet’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... NOTE Call with DUP: .Call("MINempirical", mat, nat, N, n1, n2, DUP = FALSE) DUP is no longer supported and will be ignored. * checking R code for possible problems ... NOTE gene.pvalue : fi: warning in matrix(1:nrow(EXP), nc = 1): partial argument match of 'nc' to 'ncol' gene.pvalue: warning in matrix(1:nrow(EXP), nc = 1): partial argument match of 'nc' to 'ncol' gene.pvalue : fi: warning in matrix(1:ncol(real), nc = 1): partial argument match of 'nc' to 'ncol' gene.pvalue: warning in matrix(1:nrow(real), nc = 1): partial argument match of 'nc' to 'ncol' gene.pvalue : fi1: warning in matrix(1:ncol(real), nc = 1): partial argument match of 'nc' to 'ncol' gene.trait.pvalue: warning in matrix(0, nr = nrow(EXP), nc = nrow(trait)): partial argument match of 'nr' to 'nrow' gene.trait.pvalue: warning in matrix(0, nr = nrow(EXP), nc = nrow(trait)): partial argument match of 'nc' to 'ncol' gene.trait.pvalue : fi: warning in matrix(1:nrow(trait), nc = 1): partial argument match of 'nc' to 'ncol' gene.trait.pvalue: warning in matrix(1:nrow(EXP), nc = 1): partial argument match of 'nc' to 'ncol' gene.trait.pvalue : fi: warning in matrix(1:ncol(real), nc = 1): partial argument match of 'nc' to 'ncol' gene.trait.pvalue: warning in matrix(1:nrow(real), nc = 1): partial argument match of 'nc' to 'ncol' gene.trait.pvalue : fj: warning in matrix(1:nrow(real), nc = 1): partial argument match of 'nc' to 'ncol' gene.trait.pvalue: warning in matrix(1:ncol(real), nc = 1): partial argument match of 'nc' to 'ncol' gene.pvalue: multiple local function definitions for ‘fi’ with different formal arguments gene.similarity : s.similarity: no visible global function definition for ‘build.mim’ gene.similarity : s.similarity: no visible global function definition for ‘mrnet’ gene.similarity : s.similarity: no visible global function definition for ‘aracne’ gene.similarity : s.similarity: no visible global function definition for ‘clr’ gene.trait.pvalue: multiple local function definitions for ‘fi’ with different formal arguments Undefined global functions or variables: aracne build.mim clr mrnet * 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 vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘bus.rnw’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/BUS.Rcheck/00check.log’ for details.
BUS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL BUS ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘BUS’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c BUS.cpp -o BUS.o BUS.cpp: In function ‘SEXPREC* MINempirical(SEXP, SEXP, SEXP, SEXP, SEXP)’: BUS.cpp:22:7: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 22 | for( int i=0; i<*ncols1; ++i ) | ^~~ In file included from /home/biocbuild/bbs-3.17-bioc/R/include/Rdefines.h:41, from BUS.h:9, from BUS.cpp:1: /home/biocbuild/bbs-3.17-bioc/R/include/Rinternals.h:369:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 369 | #define UNPROTECT(n) Rf_unprotect(n) | ^~~~~~~~~~~~ BUS.cpp:27:10: note: in expansion of macro ‘UNPROTECT’ 27 | UNPROTECT(6); | ^~~~~~~~~ g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o BUS.so BUS.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BUS/00new/BUS/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 (BUS)
BUS.Rcheck/BUS-Ex.timings
name | user | system | elapsed | |
BUS | 0.063 | 0.000 | 0.062 | |
gene.pvalue | 1.262 | 0.032 | 1.294 | |
gene.similarity | 0.004 | 0.000 | 0.004 | |
gene.trait.pvalue | 1.006 | 0.003 | 1.011 | |
gene.trait.similarity | 0.015 | 0.001 | 0.016 | |
pred.network | 1.313 | 0.000 | 1.313 | |
tumors.mRNA | 0.010 | 0.003 | 0.013 | |
tumors.miRNA | 0.002 | 0.001 | 0.002 | |