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BioC 3.5: CHECK report for deepSNV on tokay2

This page was generated on 2017-10-18 14:21:41 -0400 (Wed, 18 Oct 2017).

Package 327/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
deepSNV 1.22.0
Moritz Gerstung
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/deepSNV
Branch: RELEASE_3_5
Last Commit: c7ce3a8
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  ERROR  skipped  skipped 

Summary

Package: deepSNV
Version: 1.22.0
Command: rm -rf deepSNV.buildbin-libdir deepSNV.Rcheck && mkdir deepSNV.buildbin-libdir deepSNV.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=deepSNV.buildbin-libdir deepSNV_1.22.0.tar.gz >deepSNV.Rcheck\00install.out 2>&1 && cp deepSNV.Rcheck\00install.out deepSNV-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=deepSNV.buildbin-libdir --install="check:deepSNV-install.out" --force-multiarch --no-vignettes --timings deepSNV_1.22.0.tar.gz
StartedAt: 2017-10-17 23:13:55 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 23:20:17 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 381.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: deepSNV.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf deepSNV.buildbin-libdir deepSNV.Rcheck && mkdir deepSNV.buildbin-libdir deepSNV.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=deepSNV.buildbin-libdir deepSNV_1.22.0.tar.gz >deepSNV.Rcheck\00install.out 2>&1 && cp deepSNV.Rcheck\00install.out deepSNV-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=deepSNV.buildbin-libdir --install="check:deepSNV-install.out" --force-multiarch --no-vignettes --timings deepSNV_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/deepSNV.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'deepSNV/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'deepSNV' version '1.22.0'
* 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 whether package 'deepSNV' can be installed ... WARNING
Found the following significant warnings:
  bam2R.cpp:69:1: warning: no return statement in function returning non-void [-Wreturn-type]
See 'C:/Users/biocbuild/bbs-3.5-bioc/meat/deepSNV.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
.deepSNVsingle: no visible global function definition for 'pchisq'
.estimateDispersion: no visible global function definition for
  'optimize'
.significantSNV: no visible global function definition for 'p.adjust'
.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<-'
bbb: no visible global function definition for 'na.omit'
betabinLRT: no visible global function definition for 'pchisq'
betabinLRT: no visible global function definition for 'p.adjust'
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'
manhattanPlot: no visible global function definition for 'legend'
mcChunk: no visible global function definition for 'mclapply'
mutID: no visible global function definition for 'seqnames'
p.combine: no visible global function definition for 'pgamma'
plot.deepSNV: no visible global function definition for 'legend'
plot.deepSNV: no visible global function definition for 'par'
plot.deepSNV: no visible global function definition for 'abline'
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<-'
PCRTest,matrix-matrix: no visible global function definition for
  'pnorm'
estimateDirichlet,matrix: no visible binding for global variable
  'dirichlet'
estimateDirichlet,matrix: no visible global function definition for
  'coefficients'
normalize,matrix-matrix : <anonymous>: no visible global function
  definition for 'loess'
overDispersion,matrix-matrix: no visible global function definition for
  'optimize'
overDispersion,matrix-matrix : <anonymous>: no visible global function
  definition for 'na.omit'
Undefined global functions or variables:
  DataFrame GRanges IRanges SimpleList VCF abline coefficients
  dirichlet info legend loess mclapply metadata metadata<- na.omit
  optimize p.adjust par pchisq pgamma pnorm scanVcfHeader seqnames
Consider adding
  importFrom("graphics", "abline", "legend", "par")
  importFrom("stats", "coefficients", "loess", "na.omit", "optimize",
             "p.adjust", "pchisq", "pgamma", "pnorm")
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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.5-bioc/meat/deepSNV.buildbin-libdir/deepSNV/libs/i386/deepSNV.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'putchar', possibly from 'putchar' (C)
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
  Found 'rand', possibly from 'rand' (C)

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.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
RCC                        8.09   0.24    8.33
estimateDispersion-methods 5.56   0.04    5.61
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
    user system elapsed
RCC 7.36   0.24    7.59
* 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: 1 WARNING, 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/deepSNV.Rcheck/00check.log'
for details.

deepSNV.Rcheck/00install.out:


install for i386

* installing *source* package 'deepSNV' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rhtslib/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c bam2R.cpp -o bam2R.o
bam2R.cpp: In function 'int bam2R_pileup_function(const bam_pileup1_t*, int, int, nttable_t)':
bam2R.cpp:69:1: warning: no return statement in function returning non-void [-Wreturn-type]
 }
 ^
bam2R.cpp: In function 'int bam2R(char**, char**, int*, int*, int*, int*, int*, int*, int*, int*, int*, int*)':
bam2R.cpp:76:13: warning: unused variable 'iter' [-Wunused-variable]
  hts_itr_t *iter = NULL;
             ^
bam2R.cpp:79:6: warning: unused variable 'c' [-Wunused-variable]
  int c = 0;
      ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rhtslib/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c betabinom.c -o betabinom.o
betabinom.c: In function 'pbb':
betabinom.c:27:9: warning: unused variable 'log' [-Wunused-variable]
  int i, log=0;
         ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o deepSNV.dll tmp.def bam2R.o betabinom.o -LC:/Users/biocbuild/bbs-3.5-bioc/R/library/Rhtslib/lib/i386 -lhts -lz -pthread -lws2_32 -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/deepSNV.buildbin-libdir/deepSNV/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'deepSNV' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rhtslib/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c bam2R.cpp -o bam2R.o
bam2R.cpp: In function 'int bam2R_pileup_function(const bam_pileup1_t*, int, int, nttable_t)':
bam2R.cpp:69:1: warning: no return statement in function returning non-void [-Wreturn-type]
 }
 ^
bam2R.cpp: In function 'int bam2R(char**, char**, int*, int*, int*, int*, int*, int*, int*, int*, int*, int*)':
bam2R.cpp:76:13: warning: unused variable 'iter' [-Wunused-variable]
  hts_itr_t *iter = NULL;
             ^
bam2R.cpp:79:6: warning: unused variable 'c' [-Wunused-variable]
  int c = 0;
      ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rhtslib/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c betabinom.c -o betabinom.o
betabinom.c: In function 'pbb':
betabinom.c:27:9: warning: unused variable 'log' [-Wunused-variable]
  int i, log=0;
         ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o deepSNV.dll tmp.def bam2R.o betabinom.o -LC:/Users/biocbuild/bbs-3.5-bioc/R/library/Rhtslib/lib/x64 -lhts -lz -pthread -lws2_32 -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/deepSNV.buildbin-libdir/deepSNV/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'deepSNV' as deepSNV_1.22.0.zip
* DONE (deepSNV)

deepSNV.Rcheck/examples_i386/deepSNV-Ex.timings:

nameusersystemelapsed
Extract-methods0.040.000.03
RCC8.090.248.33
RF0.010.000.01
bam2R0.020.000.02
betabinLRT000
consensusSequence-methods0.010.000.01
control-methods0.020.000.02
coordinates-methods0.010.000.01
counts0.020.000.02
deepSNV-class0.340.060.41
deepSNV-methods0.280.000.28
deepSNV-package0.220.030.25
estimateDirichlet-methods3.820.083.89
estimateDispersion-methods5.560.045.61
makePrior000
manhattanPlot0.140.000.14
normalize-methods2.760.022.78
p.combine0.160.000.16
p.val-methods0.000.010.02
phiX2.410.002.40
pi0.060.000.06
plot.deepSNV0.190.030.22
repeatMask-methods1.080.021.09
shearwater1.190.001.19
show-deepSNV-method0.260.010.28
summary-methods0.270.000.27
test-methods000
trueSNVs0.010.040.04

deepSNV.Rcheck/examples_x64/deepSNV-Ex.timings:

nameusersystemelapsed
Extract-methods0.010.000.02
RCC7.360.247.59
RF000
bam2R0.010.000.02
betabinLRT000
consensusSequence-methods0.020.010.03
control-methods000
coordinates-methods000
counts0.040.000.03
deepSNV-class0.350.000.36
deepSNV-methods0.250.000.25
deepSNV-package0.180.030.20
estimateDirichlet-methods3.720.073.78
estimateDispersion-methods4.560.034.60
makePrior000
manhattanPlot0.140.000.14
normalize-methods2.110.012.12
p.combine0.120.020.14
p.val-methods000
phiX2.170.032.21
pi0.070.000.06
plot.deepSNV0.220.000.22
repeatMask-methods1.20.01.2
shearwater0.860.000.86
show-deepSNV-method0.190.020.20
summary-methods0.180.010.21
test-methods0.020.000.01
trueSNVs0.010.020.03