Back to the "Multiple platform build/check report" A  B  C  D  E  F  G [H] I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 2.13: CHECK report for Harshlight on zin1

This page was generated on 2014-04-05 09:47:21 -0700 (Sat, 05 Apr 2014).

Package 339/750HostnameOS / ArchBUILDCHECKBUILD BIN
Harshlight 1.34.0
Maurizio Pellegrino
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/Harshlight
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: Harshlight
Version: 1.34.0
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings Harshlight_1.34.0.tar.gz
StartedAt: 2014-04-05 01:49:08 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 01:50:38 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 90.2 seconds
RetCode: 0
Status:  OK 
CheckDir: Harshlight.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/Harshlight.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Harshlight/DESCRIPTION’ ... OK
* this is package ‘Harshlight’ version ‘1.34.0’
* 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 ‘Harshlight’ can be installed ... [9s/9s] 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 ... NOTE
Harshlight: no visible binding for global variable ‘sim’
Harshlight: no visible binding for global variable ‘sim.int’
* 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 line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘/home/biocbuild/bbs-2.13-bioc/meat/Harshlight.Rcheck/Harshlight/libs/Harshlight.so’:
  Found ‘stderr’, possibly from ‘stderr’ (C)
    Object: ‘Harshlight.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘Harshlight.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [5s/5s] 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

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/Harshlight.Rcheck/00check.log’
for details.

Harshlight.Rcheck/00install.out:

* installing *source* package ‘Harshlight’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c Harshlight.c -o Harshlight.o
Harshlight.c: In function ‘extended_defects’:
Harshlight.c:564:20: warning: variable ‘p_num_points’ set but not used [-Wunused-but-set-variable]
Harshlight.c: In function ‘image_dilation’:
Harshlight.c:948:10: warning: variable ‘cell_value’ set but not used [-Wunused-but-set-variable]
Harshlight.c: In function ‘norm’:
Harshlight.c:1316:27: warning: unused variable ‘sorted2’ [-Wunused-variable]
Harshlight.c: In function ‘report_overall_header’:
Harshlight.c:1471:3: warning: unknown conversion type character ‘)’ in format [-Wformat]
Harshlight.c:1474:3: warning: unknown conversion type character ‘)’ in format [-Wformat]
Harshlight.c: In function ‘chip_summary’:
Harshlight.c:1532:3: warning: unknown conversion type character ‘)’ in format [-Wformat]
Harshlight.c:1542:3: warning: unknown conversion type character ‘)’ in format [-Wformat]
Harshlight.c:1543:3: warning: unknown conversion type character ‘)’ in format [-Wformat]
Harshlight.c: In function ‘extended_stop’:
Harshlight.c:1555:3: warning: unknown conversion type character ‘)’ in format [-Wformat]
gcc -std=gnu99 -shared -L/usr/local/lib -o Harshlight.so Harshlight.o -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-bioc/meat/Harshlight.Rcheck/Harshlight/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Harshlight)

Harshlight.Rcheck/Harshlight-Ex.timings:

nameusersystemelapsed
Harshlight0.1440.0040.146