BioC 3.2: CHECK report for ACME on zin1

Package: ACME

Version: 2.26.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ACME_2.26.0.tar.gz

StartedAt: 2016-04-22 21:55:24 -0700 (Fri, 22 Apr 2016)

EndedAt: 2016-04-22 21:56:17 -0700 (Fri, 22 Apr 2016)

EllapsedTime: 52.9 seconds

RetCode: 0

Status:  OK

CheckDir: ACME.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ACME_2.26.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/ACME.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ACME/DESCRIPTION’ ... OK
* this is package ‘ACME’ version ‘2.26.0’
* 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 ‘ACME’ can be installed ... [2s/2s] OK
* checking installed package size ... NOTE
  installed size is 30.9Mb
  sub-directories of 1Mb or more:
    data      3.1Mb
    extdata  27.3Mb
* 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
findClosestGene: no visible binding for global variable ‘refflat’
findClosestGene: no visible binding for '<<-' assignment to ‘refflat’
* 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 ... [27s/28s] 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/ACME.Rcheck/00check.log’
for details.

* installing *source* package ‘ACME’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c windowChisq.c -o windowChisq.o
windowChisq.c: In function ‘windowChisq’:
windowChisq.c:58:14: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
    firstprobe>0) {
              ^
windowChisq.c:63:13: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
    lastprobe<(na-1)) {
             ^
windowChisq.c:21:11: warning: unused variable ‘xa’ [-Wunused-variable]
   double *xa,*xlocations,*xchivals;
           ^
windowChisq.c: At top level:
windowChisq.c:86:5: warning: initialization from incompatible pointer type [enabled by default]
     {"windowChisq",&windowChisq,5},
     ^
windowChisq.c:86:5: warning: (near initialization for ‘callMethods[0].fun’) [enabled by default]
gcc -std=gnu99 -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o ACME.so windowChisq.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-bioc/meat/ACME.Rcheck/ACME/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘print’ from package ‘base’ in package ‘ACME’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ACME)

name	user	system	elapsed
ACMECalcSet-class	2.795	0.056	2.865
ACMESet-class	0.530	0.004	0.535
aGFF-class	0.527	0.004	0.532
aGFFCalc-class	2.413	0.016	2.438
do.aGFF.calc	2.345	0.012	2.374
example.agff	0.648	0.012	0.658
findClosestGene	2.096	0.016	2.659
findRegions	3.914	0.028	3.947
generics	0.530	0.004	0.538
getRefflat	1.954	0.032	2.530
read.resultsGFF	4.333	0.040	4.391
write.bedGraph	1.931	0.016	1.948
write.sgr	1.891	0.020	1.939