Package: deepSNV

Version: 1.32.0

Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:deepSNV.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings deepSNV_1.32.0.tar.gz

StartedAt: 2020-04-15 02:31:54 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 02:39:34 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 460.5 seconds

RetCode: 0

Status:  OK

CheckDir: deepSNV.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:deepSNV.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings deepSNV_1.32.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/deepSNV.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.32.0'
* 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 ... OK
* checking installed package size ... NOTE
  installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
* 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.
Versioned 'LinkingTo' value for 'Rhtslib' is only usable in R >= 3.0.2
* 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<-'
bf2Vcf: no visible global function definition for 'meta'
bf2Vcf: no visible global function definition for 'meta<-'
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<-'
qvals2Vcf: no visible global function definition for 'meta'
qvals2Vcf: no visible global function definition for 'meta<-'
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 meta meta<- 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 ... NOTE
GNU make is a SystemRequirements.
* 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-3.10-bioc/R/library/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)
File 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/deepSNV/libs/x64/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 use Fortran I/O
nor system RNGs. 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
RCC                        9.39   0.31    9.71
estimateDispersion-methods 6.33   0.08    6.40
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
    user system elapsed
RCC 7.37   0.14    7.52
* 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: 7 NOTEs
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/deepSNV.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/deepSNV_1.32.0.tar.gz && rm -rf deepSNV.buildbin-libdir && mkdir deepSNV.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=deepSNV.buildbin-libdir deepSNV_1.32.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL deepSNV_1.32.0.zip && rm deepSNV_1.32.0.tar.gz deepSNV_1.32.0.zip
###
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100 1275k  100 1275k    0     0  5246k      0 --:--:-- --:--:-- --:--:-- 5337k

install for i386

* installing *source* package 'deepSNV' ...
** using staged installation

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


** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c bam2R.cpp -o bam2R.o
bam2R.cpp: In function 'int bam2R(char**, char**, int*, int*, int*, int*, int*, int*, int*, int*, int*, int*)':
bam2R.cpp:96:13: warning: unused variable 'iter' [-Wunused-variable]
  hts_itr_t *iter = NULL;
             ^
bam2R.cpp:99:6: warning: unused variable 'c' [-Wunused-variable]
  int c = 0;
      ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/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++ -std=gnu++11 -shared -s -static-libgcc -o deepSNV.dll tmp.def bam2R.o betabinom.o C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/usrlib/i386/libhts.a -LC:/extsoft/lib/i386 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -lidn -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/deepSNV.buildbin-libdir/00LOCK-deepSNV/00new/deepSNV/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'deepSNV'
    finding HTML links ... done
    Extract-methods                         html  
    RCC                                     html  
    RF                                      html  
    bam2R                                   html  
    betabinLRT                              html  
    bf2Vcf                                  html  
    finding level-2 HTML links ... done

    consensusSequence-methods               html  
    control-methods                         html  
    coordinates-methods                     html  
    counts                                  html  
    dbetabinom                              html  
    deepSNV-class                           html  
    deepSNV-methods                         html  
    deepSNV-package                         html  
    estimateDirichlet-methods               html  
    estimateDispersion-methods              html  
    estimateRho                             html  
    loadAllData                             html  
    makePrior                               html  
    manhattanPlot                           html  
    mcChunk                                 html  
    normalize-methods                       html  
    p.combine                               html  
    p.val-methods                           html  
    pbetabinom                              html  
    phiX                                    html  
    pi                                      html  
    plot.deepSNV                            html  
    qvals2Vcf                               html  
    repeatMask-methods                      html  
    shearwater                              html  
    show-deepSNV-method                     html  
    summary-methods                         html  
    test-methods                            html  
    trueSNVs                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

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++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c bam2R.cpp -o bam2R.o
bam2R.cpp: In function 'int bam2R(char**, char**, int*, int*, int*, int*, int*, int*, int*, int*, int*, int*)':
bam2R.cpp:96:13: warning: unused variable 'iter' [-Wunused-variable]
  hts_itr_t *iter = NULL;
             ^
bam2R.cpp:99:6: warning: unused variable 'c' [-Wunused-variable]
  int c = 0;
      ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/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++ -std=gnu++11 -shared -s -static-libgcc -o deepSNV.dll tmp.def bam2R.o betabinom.o C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -LC:/extsoft/lib/x64 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/deepSNV.buildbin-libdir/deepSNV/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'deepSNV' as deepSNV_1.32.0.zip
* DONE (deepSNV)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'deepSNV' successfully unpacked and MD5 sums checked