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This page was generated on 2021-10-13 15:05:03 -0400 (Wed, 13 Oct 2021).

CHECK results for MANOR on nebbiolo1

To the developers/maintainers of the MANOR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MANOR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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 1027/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MANOR 1.64.0  (landing page)
Pierre Neuvial
Snapshot Date: 2021-10-12 04:50:13 -0400 (Tue, 12 Oct 2021)
git_url: https://git.bioconductor.org/packages/MANOR
git_branch: RELEASE_3_13
git_last_commit: 6c2e394
git_last_commit_date: 2021-05-19 11:36:36 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MANOR
Version: 1.64.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:MANOR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings MANOR_1.64.0.tar.gz
StartedAt: 2021-10-12 10:35:01 -0400 (Tue, 12 Oct 2021)
EndedAt: 2021-10-12 10:35:31 -0400 (Tue, 12 Oct 2021)
EllapsedTime: 29.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MANOR.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:MANOR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings MANOR_1.64.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/MANOR.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.64.0’
* 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 ... WARNING
Found the following significant warnings:
  /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output may be truncated copying 100 bytes from a string of length 100 [-Wstringop-truncation]
See ‘/home/biocbuild/bbs-3.13-bioc/meat/MANOR.Rcheck/00install.out’ for details.
* 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 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/MANOR.Rcheck/00check.log’
for details.



Installation output

MANOR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL MANOR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘MANOR’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.13-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-3.13-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-3.13-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-3.13-bioc/R/include/R.h:86,
                 from exememo.c:20:
exememo.c: In function ‘GenAlloc’:
/home/biocbuild/bbs-3.13-bioc/R/include/R_ext/Error.h:52:15: warning: ‘msg’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   52 | #define error Rf_error
      |               ^~~~~~~~
exememo.c:39:11: note: ‘msg’ was declared here
   39 |     char* msg;
      |           ^~~
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c nem_alg.c -o nem_alg.o
In file included from /usr/include/string.h:495,
                 from nem_alg.c:72:
In function ‘strncpy’,
    inlined from ‘ClassifyByNemHeuBeta’ at nem_alg.c:801:7,
    inlined from ‘ClassifyByNem’ at nem_alg.c:578:13:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output may be truncated copying 100 bytes from a string of length 100 [-Wstringop-truncation]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.13-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-3.13-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-3.13-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-3.13-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-3.13-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-3.13-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c registerDynamicSymbols.c -o registerDynamicSymbols.o
gcc -shared -L/home/biocbuild/bbs-3.13-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-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-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
arrayTrend0.3010.0080.309
detectSB0.2890.0240.312
flag.arrayCGH0.8200.0040.825
flag.summary0.0870.0040.091
flags0.0880.0000.088
genome.plot0.3060.0040.310
import0.1350.0000.135
nem0.9790.0000.978
norm3.2050.0163.221
qscore.arrayCGH0.0880.0000.087
qscore.summary0.2910.0090.300
qscores0.2970.0040.299
report.plot0.9260.0140.941
sort0.3180.0110.329
spatial0.2660.0130.278
to.flag0.3620.0120.374