Stefano Calza
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/LVSmiRNA |
| Branch: RELEASE_3_9 |
| Last Commit: 621cd5f |
| Last Changed Date: 2019-05-02 11:53:18 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:24:19 -0400 (Wed, 16 Oct 2019).
| Package 894/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| LVSmiRNA 1.34.0 Stefano Calza
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: LVSmiRNA |
| Version: 1.34.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:LVSmiRNA.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings LVSmiRNA_1.34.0.tar.gz |
| StartedAt: 2019-10-16 04:51:41 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 04:53:39 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 117.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: LVSmiRNA.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:LVSmiRNA.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings LVSmiRNA_1.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/LVSmiRNA.Rcheck' * using R version 3.6.1 (2019-07-05) * 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 '1.34.0' * 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 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 ... NOTE Found the following apparent S3 methods exported but not registered: estVC.EList estVC.RGList See section 'Registering S3 methods' in the 'Writing R Extensions' manual. * 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-3.9-bioc/R/library/LVSmiRNA/libs/i386/LVSmiRNA.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/LVSmiRNA/libs/x64/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, 4 NOTEs See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/LVSmiRNA.Rcheck/00check.log' for details.
LVSmiRNA.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/LVSmiRNA_1.34.0.tar.gz && rm -rf LVSmiRNA.buildbin-libdir && mkdir LVSmiRNA.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=LVSmiRNA.buildbin-libdir LVSmiRNA_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL LVSmiRNA_1.34.0.zip && rm LVSmiRNA_1.34.0.tar.gz LVSmiRNA_1.34.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
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install for i386
* installing *source* package 'LVSmiRNA' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-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-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-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-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-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-3~1.9-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lRblas -LC:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/LVSmiRNA.buildbin-libdir/00LOCK-LVSmiRNA/00new/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 from temporary location
No methods found in package 'BiocGenerics' for requests: 'as.vector', 'unlist' when loading 'LVSmiRNA'
** testing if installed package can be loaded from final location
No methods found in package 'BiocGenerics' for requests: 'as.vector', 'unlist' when loading 'LVSmiRNA'
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'LVSmiRNA' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-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-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-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-3.9-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.9-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-3~1.9-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lRblas -LC:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-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_1.34.0.zip
* DONE (LVSmiRNA)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'LVSmiRNA' successfully unpacked and MD5 sums checked
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LVSmiRNA.Rcheck/examples_i386/LVSmiRNA-Ex.timings
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LVSmiRNA.Rcheck/examples_x64/LVSmiRNA-Ex.timings
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