Alejandro Caceres
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/inveRsion |
| Branch: RELEASE_3_9 |
| Last Commit: 2bc6b77 |
| Last Changed Date: 2019-05-02 11:53:22 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:24:50 -0400 (Wed, 16 Oct 2019).
| Package 825/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| inveRsion 1.32.0 Alejandro Caceres
| 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 | OK | OK | |
| Package: inveRsion |
| Version: 1.32.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:inveRsion.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings inveRsion_1.32.0.tar.gz |
| StartedAt: 2019-10-16 04:36:35 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 04:38:34 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 119.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: inveRsion.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:inveRsion.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings inveRsion_1.32.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/inveRsion.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 'inveRsion/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'inveRsion' version '1.32.0'
* 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 'inveRsion' can be installed ... WARNING
Found the following significant warnings:
inversionModel.c:185:31: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
inversionModel.c:360:15: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/inveRsion.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
'methods'
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
Package in Depends field not imported from: 'haplo.stats'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File 'inveRsion/R/zzz.R':
.onLoad calls:
packageStartupMessage("\n")
packageStartupMessage("Hola!\n")
packageStartupMessage("welcome to inevRsion package. \n \n \n")
packageStartupMessage("type: manual() for full manual \n vignette(\"inveRsion\") for a quick start \n")
See section 'Good practice' in '?.onAttach'.
callEncode: no visible global function definition for 'quantile'
encodeGeno: no visible global function definition for 'setupGeno'
encodeGeno: no visible global function definition for 'haplo.em'
encodeGeno: no visible global function definition for
'haplo.em.control'
encodeGenoAcross: no visible global function definition for 'setupGeno'
encodeGenoAcross: no visible global function definition for 'haplo.em'
encodeGenoAcross: no visible global function definition for
'haplo.em.control'
Undefined global functions or variables:
haplo.em haplo.em.control quantile setupGeno
Consider adding
importFrom("stats", "quantile")
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 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-3.9-bioc/R/library/inveRsion/libs/i386/inveRsion.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/inveRsion/libs/x64/inveRsion.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/inveRsion.Rcheck/00check.log'
for details.
inveRsion.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/inveRsion_1.32.0.tar.gz && rm -rf inveRsion.buildbin-libdir && mkdir inveRsion.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=inveRsion.buildbin-libdir inveRsion_1.32.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL inveRsion_1.32.0.zip && rm inveRsion_1.32.0.tar.gz inveRsion_1.32.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 449k 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 449k 100 449k 0 0 8937k 0 --:--:-- --:--:-- --:--:-- 9571k
install for i386
* installing *source* package 'inveRsion' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c init_inveRsion.c -o init_inveRsion.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c inversionModel.c -o inversionModel.o
inversionModel.c: In function 'blockAndLev':
inversionModel.c:185:31: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
if(dat[(*nr)*(c1)+row]==levelleft[level] & dat[(*nr)*(c2)+row]==levelright[level])
^
inversionModel.c: In function 'inversionModel':
inversionModel.c:360:15: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
while(steps<*maxSteps & tol>mintol)
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c writeGenoDat.c -o writeGenoDat.o
writeGenoDat.c: In function 'writeGenoDat':
writeGenoDat.c:34:16: warning: 'dat' may be used uninitialized in this function [-Wmaybe-uninitialized]
int i,j,l,k,dat,nomiss[*numlevcaco],sum[*numlevcaco];
^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o inveRsion.dll tmp.def init_inveRsion.o inversionModel.o writeGenoDat.o -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 -lgfortran -lm -lquadmath -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/inveRsion.buildbin-libdir/00LOCK-inveRsion/00new/inveRsion/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'inveRsion'
finding HTML links ... done
GenoDat-class html
GenoDatROI-class html
HaploCode-class html
ac html
accBic html
accuracy-class html
codeHaplo html
gDat html
getClassif-methods html
getInv-methods html
getROIs-methods html
hapCode html
invList html
inveRsion-internal html
inveRsion-package html
inversion-class html
inversionList-class html
listInv-methods html
scan-class html
scanInv html
scanRes html
setUpGenoDatFile 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 'inveRsion' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c init_inveRsion.c -o init_inveRsion.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c inversionModel.c -o inversionModel.o
inversionModel.c: In function 'blockAndLev':
inversionModel.c:185:31: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
if(dat[(*nr)*(c1)+row]==levelleft[level] & dat[(*nr)*(c2)+row]==levelright[level])
^
inversionModel.c: In function 'inversionModel':
inversionModel.c:360:15: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
while(steps<*maxSteps & tol>mintol)
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c writeGenoDat.c -o writeGenoDat.o
writeGenoDat.c: In function 'writeGenoDat':
writeGenoDat.c:34:16: warning: 'dat' may be used uninitialized in this function [-Wmaybe-uninitialized]
int i,j,l,k,dat,nomiss[*numlevcaco],sum[*numlevcaco];
^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o inveRsion.dll tmp.def init_inveRsion.o inversionModel.o writeGenoDat.o -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 -lgfortran -lm -lquadmath -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/inveRsion.buildbin-libdir/inveRsion/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'inveRsion' as inveRsion_1.32.0.zip
* DONE (inveRsion)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'inveRsion' successfully unpacked and MD5 sums checked
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inveRsion.Rcheck/examples_i386/inveRsion-Ex.timings
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inveRsion.Rcheck/examples_x64/inveRsion-Ex.timings
|