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BioC 3.4: CHECK report for GraphAlignment on malbec1

This page was generated on 2017-04-15 16:09:35 -0400 (Sat, 15 Apr 2017).

Package 556/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GraphAlignment 1.38.0
Joern P. Meier
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/GraphAlignment
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GraphAlignment
Version: 1.38.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings GraphAlignment_1.38.0.tar.gz
StartedAt: 2017-04-14 23:02:23 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 23:02:40 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 16.5 seconds
RetCode: 0
Status:  OK 
CheckDir: GraphAlignment.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings GraphAlignment_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/GraphAlignment.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GraphAlignment/DESCRIPTION’ ... OK
* this is package ‘GraphAlignment’ version ‘1.38.0’
* 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 ‘GraphAlignment’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... OK
* checking R code for possible problems ... NOTE
File ‘GraphAlignment/R/GraphAlignment.R’:
  .Last.lib calls:
    library.dynam.unload("GraphAlignment", libpath)

Package detach functions should not call ‘library.dynam.unload’.
See section ‘Good practice’ in '?.Last.lib'.

AlignNetworks: no visible global function definition for ‘rnorm’
GenerateExample: no visible global function definition for ‘runif’
GenerateExample: no visible global function definition for ‘rnorm’
GenerateExample: no visible global function definition for ‘pnorm’
InitialAlignment: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  pnorm rnorm runif
Consider adding
  importFrom("stats", "pnorm", "rnorm", "runif")
to your NAMESPACE file.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
File ‘GraphAlignment/libs/GraphAlignment.so’:
  Found ‘putchar’, possibly from ‘putchar’ (C)
    Object: ‘lap.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* 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-3.4-bioc/meat/GraphAlignment.Rcheck/00check.log’
for details.


GraphAlignment.Rcheck/00install.out:

* installing *source* package ‘GraphAlignment’ ...
** libs
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c GA_alloc.c -o GA_alloc.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c GA_matrix.c -o GA_matrix.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c GA_matrix_R.c -o GA_matrix_R.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c GA_message.c -o GA_message.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c GA_vector.c -o GA_vector.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c GA_vector_R.c -o GA_vector_R.o
GA_vector_R.c: In function ‘GA_clamp_mode_from_R’:
GA_vector_R.c:139:9: warning: unused variable ‘size’ [-Wunused-variable]
     int size = LENGTH(robj);
         ^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c GraphAlignment.c -o GraphAlignment.o
GraphAlignment.c: In function ‘GA_encode_directed_graph’:
GraphAlignment.c:138:20: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wparentheses]
                 if (matrix->elts[i][j] == 1)
                    ^
GraphAlignment.c:159:20: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wparentheses]
                 if (matrix->elts[i][j] == 1)
                    ^
GraphAlignment.c: In function ‘GA_directed_mode_from_R’:
GraphAlignment.c:264:9: warning: unused variable ‘size’ [-Wunused-variable]
     int size = LENGTH(robj);
         ^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c lap.c -o lap.o
lap.c: In function ‘LAP_checklap’:
lap.c:348:9: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result]
         scanf("%c", &wait);
         ^
lap.c:358:7: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result]
       scanf("%c", &wait);
       ^
lap.c:371:7: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result]
       scanf("%c", &wait);
       ^
lap.c:384:7: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result]
       scanf("%c", &wait);
       ^
lap.c:394:7: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result]
       scanf("%c", &wait);
       ^
lap.c: In function ‘LAP_lap’:
lap.c:64:30: warning: ‘last’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   col  j, j1, j2, endofpath, last, low, up, *collist, *matches;
                              ^
lap.c:260:11: warning: ‘min’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         h = assigncost[i][j1] - v[j1] - min;
           ^
gcc -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o GraphAlignment.so GA_alloc.o GA_matrix.o GA_matrix_R.o GA_message.o GA_vector.o GA_vector_R.o GraphAlignment.o lap.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/GraphAlignment.Rcheck/GraphAlignment/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GraphAlignment)

GraphAlignment.Rcheck/GraphAlignment-Ex.timings:

nameusersystemelapsed
AlignNetworks0.0440.0000.044
AlignedPairs0.0440.0000.041
AnalyzeAlignment0.0440.0040.046
ComputeLinkParameters0.020.000.02
ComputeM0.0320.0000.030
ComputeNodeParameters0.0040.0040.007
ComputeScores0.0880.0000.085
CreateScoreMatrix0.0000.0000.002
EncodeDirectedGraph000
GenerateExample0.0960.0000.097
GetBinNumber000
InitialAlignment0.0000.0000.002
InvertPermutation0.0000.0000.001
LinearAssignment0.0040.0000.000
MatrixToBin0.0000.0000.001
Permute0.0000.0000.001
Trace0.0000.0000.001
VectorToBin0.0000.0000.001