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CHECK report for MANOR on malbec1

This page was generated on 2020-04-15 12:04:33 -0400 (Wed, 15 Apr 2020).

Package 947/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MANOR 1.58.0
Pierre Neuvial
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/MANOR
Branch: RELEASE_3_10
Last Commit: 483c3fa
Last Changed Date: 2019-10-29 13:07:37 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  ERROR  skipped  skipped 

Summary

Package: MANOR
Version: 1.58.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:MANOR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings MANOR_1.58.0.tar.gz
StartedAt: 2020-04-15 00:17:03 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 00:17:33 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 29.9 seconds
RetCode: 0
Status:  OK 
CheckDir: MANOR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:MANOR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings MANOR_1.58.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/MANOR.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.58.0’
* 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 ‘MANOR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘GLAD’
A package should be listed in only one of these fields.
* 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  arrayTrend.arrayCGH arrayTrend.default detectSB.arrayCGH
  flag.summary.arrayCGH flag.summary.default genome.plot.arrayCGH
  genome.plot.default html.report.arrayCGH html.report.default
  nem.arrayCGH nem.default norm.arrayCGH print.flag
  report.plot.arrayCGH report.plot.default sort.arrayCGH
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* 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
File ‘/home/biocbuild/bbs-3.10-bioc/R/library/MANOR/libs/MANOR.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘srand’, possibly from ‘srand’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/MANOR.Rcheck/00check.log’
for details.



Installation output

MANOR.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL MANOR
###
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘MANOR’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.10-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-3.10-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-3.10-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-3.10-bioc/R/include/R.h:86:0,
                 from exememo.c:20:
exememo.c: In function ‘GenAlloc’:
/home/biocbuild/bbs-3.10-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-3.10-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-3.10-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-3.10-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-3.10-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-3.10-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-3.10-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c nem_ver.c -o nem_ver.o
gcc -shared -L/home/biocbuild/bbs-3.10-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 -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-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)

Tests output


Example timings

MANOR.Rcheck/MANOR-Ex.timings

nameusersystemelapsed
arrayTrend0.4520.0200.475
detectSB0.3520.0000.352
flag.arrayCGH1.0520.0081.059
flag.summary0.180.000.18
flags0.1680.0040.171
genome.plot0.4880.0040.491
import0.1600.0000.161
nem1.5440.0081.554
norm1.0680.0161.094
qscore.arrayCGH0.1680.0040.174
qscore.summary0.7120.0040.719
qscores0.6920.0000.698
report.plot0.7400.0000.742
sort0.2520.0120.267
spatial0.3640.0080.370
to.flag0.4720.0120.485