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This page was generated on 2020-10-17 11:55:03 -0400 (Sat, 17 Oct 2020).
TO THE DEVELOPERS/MAINTAINERS OF THE MANOR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 980/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
MANOR 1.60.0 Pierre Neuvial
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK |
Package: MANOR |
Version: 1.60.0 |
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:MANOR.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings MANOR_1.60.0.tar.gz |
StartedAt: 2020-10-17 02:46:36 -0400 (Sat, 17 Oct 2020) |
EndedAt: 2020-10-17 02:47:13 -0400 (Sat, 17 Oct 2020) |
EllapsedTime: 37.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MANOR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:MANOR.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings MANOR_1.60.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/MANOR.Rcheck’ * using R version 4.0.3 (2020-10-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MANOR/DESCRIPTION’ ... OK * this is package ‘MANOR’ version ‘1.60.0’ * package encoding: UTF-8 * 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 ‘MANOR’ 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 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 ‘/home/biocbuild/bbs-3.11-bioc/meat/MANOR.Rcheck/00check.log’ for details.
MANOR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL MANOR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’ * installing *source* package ‘MANOR’ ... ** using staged installation ** libs gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c Rnem_arg.c -o Rnem_arg.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c Rnem_exe.c -o Rnem_exe.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c exememo.c -o exememo.o In file included from /home/biocbuild/bbs-3.11-bioc/R/include/R.h:86:0, from exememo.c:20: exememo.c: In function ‘GenAlloc’: /home/biocbuild/bbs-3.11-bioc/R/include/R_ext/Error.h:52:15: warning: ‘msg’ may be used uninitialized in this function [-Wmaybe-uninitialized] #define error Rf_error ^~~~~~~~ exememo.c:39:11: note: ‘msg’ was declared here char* msg; ^~~ gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c nem_alg.c -o nem_alg.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c nem_hlp.c -o nem_hlp.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c nem_mod.c -o nem_mod.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c nem_nei.c -o nem_nei.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c nem_rnd.c -o nem_rnd.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c nem_ver.c -o nem_ver.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c registerDynamicSymbols.c -o registerDynamicSymbols.o gcc -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o MANOR.so Rnem_arg.o Rnem_exe.o exememo.o nem_alg.o nem_hlp.o nem_mod.o nem_nei.o nem_rnd.o nem_ver.o registerDynamicSymbols.o -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-MANOR/00new/MANOR/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 (MANOR)
MANOR.Rcheck/MANOR-Ex.timings
name | user | system | elapsed | |
arrayTrend | 0.320 | 0.004 | 0.323 | |
detectSB | 0.323 | 0.004 | 0.327 | |
flag.arrayCGH | 1.383 | 0.012 | 1.396 | |
flag.summary | 0.137 | 0.000 | 0.137 | |
flags | 0.14 | 0.00 | 0.14 | |
genome.plot | 0.446 | 0.008 | 0.453 | |
import | 0.246 | 0.000 | 0.294 | |
nem | 1.553 | 0.000 | 1.553 | |
norm | 4.108 | 0.004 | 4.112 | |
qscore.arrayCGH | 0.094 | 0.000 | 0.094 | |
qscore.summary | 0.455 | 0.004 | 0.460 | |
qscores | 0.349 | 0.000 | 0.349 | |
report.plot | 0.94 | 0.00 | 0.94 | |
sort | 0.336 | 0.004 | 0.340 | |
spatial | 0.282 | 0.008 | 0.291 | |
to.flag | 0.363 | 0.000 | 0.362 | |