Multiple platform build/check report for BioC 3.8 - CHECK report for LVSmiRNA on tokay1

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### Running command:
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###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:LVSmiRNA.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings LVSmiRNA_1.32.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/LVSmiRNA.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'LVSmiRNA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'LVSmiRNA' version '1.32.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 whether package 'LVSmiRNA' can be installed ... OK
* checking installed package size ... OK
* 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
* 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
Package in Depends field not imported from: 'splines'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: 'vsn:::vsn2trsf'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
read.mir: no visible global function definition for 'read.maimages'
Undefined global functions or variables:
  read.maimages
* 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 ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... WARNING
  apparently using $(BLAS_LIBS) without following $(FLIBS) in 'src/Makevars'
* 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-3.8-bioc/R/library/LVSmiRNA/libs/i386/LVSmiRNA.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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
** running examples for arch 'x64' ... 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: 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/LVSmiRNA.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/LVSmiRNA_1.32.0.tar.gz && rm -rf LVSmiRNA.buildbin-libdir && mkdir LVSmiRNA.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=LVSmiRNA.buildbin-libdir LVSmiRNA_1.32.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL LVSmiRNA_1.32.0.zip && rm LVSmiRNA_1.32.0.tar.gz LVSmiRNA_1.32.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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100  316k  100  316k    0     0  6514k      0 --:--:-- --:--:-- --:--:-- 7029k

install for i386

* installing *source* package 'LVSmiRNA' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c basic_fns.c -o basic_fns.o
basic_fns.c: In function 'lvs_median':
basic_fns.c:146:7: warning: unused variable 'i' [-Wunused-variable]
   int i;
       ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c lvs_rlm.c -o lvs_rlm.o
lvs_rlm.c: In function 'gamma_fit':
lvs_rlm.c:175:30: warning: variable 'converged' set but not used [-Wunused-but-set-variable]
   int i,j, rows, cols, iter, converged=0;
                              ^
lvs_rlm.c: In function 'test_gamma_fit':
lvs_rlm.c:286:30: warning: variable 'converged' set but not used [-Wunused-but-set-variable]
   int i,j, rows, cols, iter, converged=0;
                              ^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o LVSmiRNA.dll tmp.def basic_fns.o init.o lvs_rlm.o -lgfortran -lm -lquadmath -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lRblas -LC:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/LVSmiRNA.buildbin-libdir/LVSmiRNA/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'BiocGenerics' for requests: 'as.vector', 'unlist' when loading 'LVSmiRNA'
** help
*** installing help indices
  converting help for package 'LVSmiRNA'
    finding HTML links ... done
    MIR-spike-in                            html  
    RLM                                     html  
    boxplot-methods                         html  
    estVC                                   html  
    exprs-methods                           html  
    exprs_assign-methods                    html  
    featureNames-method                     html  
    lvs                                     html  
    plotRA                                  html  
    finding level-2 HTML links ... done

    preproc-methods                         html  
    preproc_assign-methods                  html  
    probeNames-methods                      html  
    read.mir                                html  
    rlmFit                                  html  
    sampleNames-methods                     html  
    summarize                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in package 'BiocGenerics' for requests: 'as.vector', 'unlist' when loading 'LVSmiRNA'
In R CMD INSTALL

install for x64

* installing *source* package 'LVSmiRNA' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c basic_fns.c -o basic_fns.o
basic_fns.c: In function 'lvs_median':
basic_fns.c:146:7: warning: unused variable 'i' [-Wunused-variable]
   int i;
       ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -DHAVE_ZLIB    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c lvs_rlm.c -o lvs_rlm.o
lvs_rlm.c: In function 'gamma_fit':
lvs_rlm.c:175:30: warning: variable 'converged' set but not used [-Wunused-but-set-variable]
   int i,j, rows, cols, iter, converged=0;
                              ^
lvs_rlm.c: In function 'test_gamma_fit':
lvs_rlm.c:286:30: warning: variable 'converged' set but not used [-Wunused-but-set-variable]
   int i,j, rows, cols, iter, converged=0;
                              ^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o LVSmiRNA.dll tmp.def basic_fns.o init.o lvs_rlm.o -lgfortran -lm -lquadmath -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lRblas -LC:/Users/biocbuild/bbs-3.8-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/LVSmiRNA.buildbin-libdir/LVSmiRNA/libs/x64
** testing if installed package can be loaded
No methods found in package 'BiocGenerics' for requests: 'as.vector', 'unlist' when loading 'LVSmiRNA'
* MD5 sums
packaged installation of 'LVSmiRNA' as LVSmiRNA_1.32.0.zip
* DONE (LVSmiRNA)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'LVSmiRNA' successfully unpacked and MD5 sums checked
In R CMD INSTALL

CHECK report for LVSmiRNA on tokay1

Summary

Command output

Installation output

Tests output

Example timings