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BioC 3.2: CHECK report for deepSNV on oaxaca

This page was generated on 2016-04-23 10:25:41 -0700 (Sat, 23 Apr 2016).

Package 259/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
deepSNV 1.16.0
Moritz Gerstung
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/deepSNV
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: deepSNV
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings deepSNV_1.16.0.tar.gz
StartedAt: 2016-04-22 23:27:50 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 23:32:25 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 275.5 seconds
RetCode: 0
Status:  OK 
CheckDir: deepSNV.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings deepSNV_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/deepSNV.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘deepSNV/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘deepSNV’ version ‘1.16.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘parallel’ ‘Rhtslib’ ‘IRanges’ ‘GenomicRanges’ ‘SummarizedExperiment’
  ‘Biostrings’ ‘VGAM’ ‘VariantAnnotation’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘deepSNV’ can be installed ... [29s/30s] 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.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Rhtslib’
A package should be listed in only one of these fields.
* 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
Packages in Depends field not imported from:
  ‘GenomicRanges’ ‘SummarizedExperiment’ ‘VariantAnnotation’ ‘parallel’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘estimateRho’ ‘logbb’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.significantSNV: no visible global function definition for ‘VCF’
.significantSNV: no visible global function definition for ‘GRanges’
.significantSNV: no visible global function definition for ‘IRanges’
.significantSNV: no visible global function definition for ‘DataFrame’
.significantSNV: no visible global function definition for ‘SimpleList’
.significantSNV: no visible global function definition for
  ‘scanVcfHeader’
.significantSNV: no visible global function definition for ‘metadata’
.significantSNV: no visible global function definition for ‘metadata<-’
bf2Vcf: no visible global function definition for ‘VCF’
bf2Vcf: no visible global function definition for ‘GRanges’
bf2Vcf: no visible global function definition for ‘IRanges’
bf2Vcf: no visible global function definition for ‘DataFrame’
bf2Vcf: no visible global function definition for ‘scanVcfHeader’
bf2Vcf: no visible global function definition for ‘SimpleList’
bf2Vcf: no visible global function definition for ‘metadata’
bf2Vcf: no visible global function definition for ‘metadata<-’
loadAllData: no visible global function definition for ‘mclapply’
makePrior: no visible global function definition for ‘info’
mcChunk: no visible global function definition for ‘mclapply’
mutID: no visible global function definition for ‘seqnames’
qvals2Vcf: no visible global function definition for ‘VCF’
qvals2Vcf: no visible global function definition for ‘GRanges’
qvals2Vcf: no visible global function definition for ‘IRanges’
qvals2Vcf: no visible global function definition for ‘DataFrame’
qvals2Vcf: no visible global function definition for ‘scanVcfHeader’
qvals2Vcf: no visible global function definition for ‘SimpleList’
qvals2Vcf: no visible global function definition for ‘metadata’
qvals2Vcf: no visible global function definition for ‘metadata<-’
estimateDirichlet,matrix: no visible binding for global variable
  ‘dirichlet’
* 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 compilation flags in Makevars ... NOTE
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work.  If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it.  If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... 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 ... [39s/39s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
RCC                        7.710  0.159   7.897
estimateDispersion-methods 5.217  0.182   5.403
estimateDirichlet-methods  4.975  0.109   5.093
* 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: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/deepSNV.Rcheck/00check.log’
for details.


deepSNV.Rcheck/00install.out:

* installing *source* package ‘deepSNV’ ...
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking malloc.h usability... no
checking malloc.h presence... no
checking for malloc.h... no
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for _LARGEFILE_SOURCE value needed for large files... no
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for working memcmp... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for off_t... yes
checking for size_t... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rhtslib/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bam2R.cpp -o bam2R.o
bam2R.cpp:43:13: warning: unused variable 'iter' [-Wunused-variable]
        hts_itr_t *iter = NULL;
                   ^
bam2R.cpp:46:6: warning: unused variable 'c' [-Wunused-variable]
        int c = 0;
            ^
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rhtslib/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c betabinom.c -o betabinom.o
betabinom.c:27:9: warning: unused variable 'log' [-Wunused-variable]
        int i, log=0;
               ^
1 warning generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o deepSNV.so bam2R.o betabinom.o -L/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rhtslib/lib -lhts -lz -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
clang: warning: argument unused during compilation: '-pthread'
installing to /Users/biocbuild/bbs-3.2-bioc/meat/deepSNV.Rcheck/deepSNV/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 (deepSNV)

deepSNV.Rcheck/deepSNV-Ex.timings:

nameusersystemelapsed
Extract-methods0.0130.0020.014
RCC7.7100.1597.897
RF0.0060.0020.008
bam2R0.0110.0010.046
betabinLRT000
consensusSequence-methods0.0300.0020.032
control-methods0.0080.0030.012
coordinates-methods0.0060.0010.008
counts0.0120.0010.013
deepSNV-class0.2620.0140.290
deepSNV-methods0.1650.0090.177
deepSNV-package0.1640.0090.176
estimateDirichlet-methods4.9750.1095.093
estimateDispersion-methods5.2170.1825.403
makePrior0.0010.0000.000
manhattanPlot0.4790.0130.508
normalize-methods1.9500.0482.007
p.combine0.1230.0080.137
p.val-methods0.0040.0010.005
phiX2.2330.0512.297
pi0.0650.0040.074
plot.deepSNV0.1480.0080.155
repeatMask-methods2.2650.0122.277
shearwater0.3660.0050.373
show-deepSNV-method0.1520.0080.160
summary-methods0.1620.0080.172
test-methods0.0050.0020.007
trueSNVs0.0350.0030.037