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BioC 3.1: CHECK report for biovizBase on zin2

This page was generated on 2015-10-09 09:24:43 -0700 (Fri, 09 Oct 2015).

Package 106/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biovizBase 1.16.0
Tengfei Yin
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/biovizBase
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: biovizBase
Version: 1.16.0
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings biovizBase_1.16.0.tar.gz
StartedAt: 2015-10-08 22:53:24 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 22:56:20 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 176.7 seconds
RetCode: 0
Status:  OK 
CheckDir: biovizBase.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings biovizBase_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/biovizBase.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biovizBase/DESCRIPTION’ ... OK
* this is package ‘biovizBase’ version ‘1.16.0’
* 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 ‘biovizBase’ can be installed ... [17s/17s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 ... NOTE
'library' or 'require' calls in package code:
  ‘BSgenome’ ‘rtracklayer’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
genSymbols: no visible binding for global variable ‘start_location’
genSymbols: no visible binding for global variable ‘end_location’
genSymbols: no visible binding for global variable ‘Chromosome’
genSymbols: no visible binding for global variable ‘symbol’
transformToLinkInCircle: no visible binding for global variable
  ‘.circle.x’
transformToLinkInCircle: no visible binding for global variable
  ‘.circle.y’
transformToLinkInCircle : <anonymous>: no visible binding for global
  variable ‘from.x’
transformToLinkInCircle : <anonymous>: no visible binding for global
  variable ‘from.y’
transformToLinkInCircle : <anonymous>: no visible binding for global
  variable ‘to.x’
transformToLinkInCircle : <anonymous>: no visible binding for global
  variable ‘to.y’
mold,ExpressionSet : .local: no visible global function definition for
  ‘exprs’
mold,ExpressionSet : .local: no visible global function definition for
  ‘pData’
mold,RleList : .local: no visible binding for global variable
  ‘xRleList’
mold,SummarizedExperiment : .local: no visible global function
  definition for ‘assays’
mold,SummarizedExperiment : .local: no visible global function
  definition for ‘colData’
mold,SummarizedExperiment : .local: no visible global function
  definition for ‘rowRanges’
mold,eSet : .local: no visible global function definition for
  ‘phenoData’
mold,eSet : .local: no visible global function definition for ‘melt’
mold,eSet : .local: no visible global function definition for
  ‘varLabels’
* 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [19s/19s] 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-3.1-bioc/meat/biovizBase.Rcheck/00check.log’
for details.


biovizBase.Rcheck/00install.out:

* installing *source* package ‘biovizBase’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_init_biovizBase.c -o R_init_biovizBase.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.1-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c bin_offsets.c -o bin_offsets.o
bin_offsets.c: In function ‘scan_bam_bin_offsets’:
bin_offsets.c:57:3: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness [-Wpointer-sign]
   if (strncmp(b, "BAI\1", 4))
   ^
In file included from /home/biocbuild/bbs-3.1-bioc/R/include/R_ext/RS.h:26:0,
                 from /home/biocbuild/bbs-3.1-bioc/R/include/Rdefines.h:26,
                 from bin_offsets.h:1,
                 from bin_offsets.c:3:
/usr/include/string.h:399:15: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
 extern size_t strlen (const char *__s)
               ^
bin_offsets.c:57:3: warning: pointer targets in passing argument 1 of ‘__builtin_strlen’ differ in signedness [-Wpointer-sign]
   if (strncmp(b, "BAI\1", 4))
   ^
bin_offsets.c:57:3: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
bin_offsets.c:57:3: warning: pointer targets in passing argument 1 of ‘__builtin_strcmp’ differ in signedness [-Wpointer-sign]
bin_offsets.c:57:3: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
bin_offsets.c:57:3: warning: pointer targets in passing argument 1 of ‘__builtin_strlen’ differ in signedness [-Wpointer-sign]
bin_offsets.c:57:3: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
bin_offsets.c:57:3: warning: pointer targets in passing argument 1 of ‘__builtin_strcmp’ differ in signedness [-Wpointer-sign]
bin_offsets.c:57:3: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
bin_offsets.c:57:3: warning: pointer targets in passing argument 1 of ‘__builtin_strcmp’ differ in signedness [-Wpointer-sign]
bin_offsets.c:57:3: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
bin_offsets.c:57:3: warning: pointer targets in passing argument 1 of ‘__builtin_strcmp’ differ in signedness [-Wpointer-sign]
bin_offsets.c:57:3: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
bin_offsets.c:57:3: warning: pointer targets in passing argument 1 of ‘strncmp’ differ in signedness [-Wpointer-sign]
In file included from /home/biocbuild/bbs-3.1-bioc/R/include/R_ext/RS.h:26:0,
                 from /home/biocbuild/bbs-3.1-bioc/R/include/Rdefines.h:26,
                 from bin_offsets.h:1,
                 from bin_offsets.c:3:
/usr/include/string.h:147:12: note: expected ‘const char *’ but argument is of type ‘Rbyte *’
 extern int strncmp (const char *__s1, const char *__s2, size_t __n)
            ^
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.1-bioc/R/lib -L/usr/local/lib -o biovizBase.so R_init_biovizBase.o bin_offsets.o -L/home/biocbuild/bbs-3.1-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.1-bioc/meat/biovizBase.Rcheck/biovizBase/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (biovizBase)

biovizBase.Rcheck/biovizBase-Ex.timings:

nameusersystemelapsed
CRC0.0060.0000.005
GCcontent0.5490.0040.552
addStepping-method0.5190.0000.519
aes-utils0.0010.0000.001
colorBlindSafePal0.0010.0000.001
containLetters0.0010.0000.001
crc1.GeRL0.0150.0000.015
crunch-method3.6140.0353.653
darned_hg19_subset5000.0360.0000.036
flatGrl0.2240.0040.229
genesymbol0.1160.0000.115
getBioColor0.0010.0000.002
getFormalNames0.0010.0000.001
getGaps1.1040.0041.114
getIdeoGR0.2730.0000.274
getIdeogram000
hg19Ideogram0.0280.0000.028
hg19IdeogramCyto0.030.000.03
ideo0.1010.0000.101
ideoCyto0.1130.0080.121
isIdeogram0.0040.0000.003
isMatchedWithModel0.3430.0040.348
isSimpleIdeogram0.0230.0000.024
maxGap-method0.3020.0000.304
pileupAsGRanges0.0000.0000.001
pileupGRangesAsVariantTable0.0010.0000.001
plotColorLegend0.0020.0000.003
scale0.2250.0040.228
showColor0.0010.0000.001
shrinkageFun-method0.2450.0080.253
splitByFacets-method0.5320.0000.542
strip_formula_dots0.0020.0000.001
subsetArgsByFormals0.0010.0000.001
transform1.7920.0721.863
transformGRangesForEvenSpace0.2160.0040.220