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BioC 2.14: CHECK report for Harshlight on zin2

This page was generated on 2014-10-08 08:48:01 -0700 (Wed, 08 Oct 2014).

Package 380/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Harshlight 1.36.0
Maurizio Pellegrino
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/Harshlight
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: Harshlight
Version: 1.36.0
Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings Harshlight_1.36.0.tar.gz
StartedAt: 2014-10-08 00:22:42 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 00:24:14 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 91.5 seconds
RetCode: 0
Status:  OK 
CheckDir: Harshlight.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings Harshlight_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/Harshlight.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.36.0’
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Calls with DUP = FALSE:
   .C("cluster_defects", img <- as.integer(img), array.size <- as.integer(array.size), 
       as.integer(size.limit), as.integer(connect), as.double(simul.pval), 
       as.double(compact.pval), as.integer(type), status <- as.integer(0), 
       DUP = FALSE, PACKAGE = "Harshlight")
   .C("diffuse_defects", img <- as.double(img), as.double(diffuse.bright), 
       as.double(-diffuse.dark), as.integer(radius), diff.bright <- as.double(diff.bright), 
       diff.dark <- as.double(diff.dark), as.double(quant), as.double(thres.dark), 
       as.double(thres.bright), status <- as.integer(0), DUP = FALSE, 
       NAOK = TRUE, PACKAGE = "Harshlight")
   .C("extended_defects", as.double(img), med.obs <- as.double(med.obs), 
       as.integer(radius), status <- as.integer(0), NAOK = TRUE, 
       DUP = FALSE, PACKAGE = "Harshlight")
   .C("image_dilation", as.double(img), result <- as.double(result), 
       as.integer(radius), status <- as.integer(0), DUP = FALSE, 
       PACKAGE = "Harshlight")
   .C("image_erosion", as.double(result), img <- as.double(img), 
       as.integer(radius), status <- as.integer(0), DUP = FALSE, 
       PACKAGE = "Harshlight")
   .C("simulations", simulation.bright <- as.integer(simulation.bright), 
       as.double(compact.quant.bright), as.integer(compact.connect), 
       status <- as.integer(0), DUP = FALSE, PACKAGE = "Harshlight")
   .C("simulations", simulation.dark <- as.integer(simulation.dark), 
       as.double(compact.quant.dark), as.integer(compact.connect), 
       status <- as.integer(0), DUP = FALSE, PACKAGE = "Harshlight")
DUP = FALSE is deprecated and may be disabled in future versions of R.
* 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-2.14-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 files in ‘vignettes’ ... OK
* checking examples ... [4s/4s] 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-2.14-bioc/meat/Harshlight.Rcheck/00check.log’
for details.

Harshlight.Rcheck/00install.out:

* installing *source* package ‘Harshlight’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.14-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-2.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.14-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
Harshlight0.0000.0000.001