Habil
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/SamSPECTRAL |
| Branch: RELEASE_3_9 |
| Last Commit: 0e5e2d9 |
| Last Changed Date: 2019-05-02 11:53:13 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:23:25 -0400 (Wed, 16 Oct 2019).
| Package 1451/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SamSPECTRAL 1.38.0 Habil
| 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: SamSPECTRAL |
| Version: 1.38.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SamSPECTRAL.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings SamSPECTRAL_1.38.0.tar.gz |
| StartedAt: 2019-10-16 06:52:45 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 06:53:24 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 38.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: SamSPECTRAL.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:SamSPECTRAL.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings SamSPECTRAL_1.38.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/SamSPECTRAL.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 'SamSPECTRAL/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SamSPECTRAL' version '1.38.0'
* 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 'SamSPECTRAL' can be installed ... OK
* 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.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
.First.lib: no visible global function definition for 'provide'
Civilized_Spectral_Clustering: no visible global function definition
for 'lm'
Civilized_Spectral_Clustering: no visible global function definition
for 'coef'
Civilized_Spectral_Clustering: no visible global function definition
for 'coefficients'
Civilized_Spectral_Clustering: no visible global function definition
for 'plot'
Civilized_Spectral_Clustering: no visible global function definition
for 'abline'
Civilized_Spectral_Clustering: no visible global function definition
for 'kmeans'
kneepointDetection: no visible global function definition for 'lm'
kneepointDetection: no visible global function definition for 'png'
kneepointDetection: no visible global function definition for 'plot'
kneepointDetection: no visible global function definition for 'par'
kneepointDetection: no visible global function definition for 'axis'
kneepointDetection: no visible global function definition for 'title'
kneepointDetection: no visible global function definition for 'abline'
kneepointDetection: no visible global function definition for 'dev.off'
Undefined global functions or variables:
abline axis coef coefficients dev.off kmeans lm par plot png provide
title
Consider adding
importFrom("grDevices", "dev.off", "png")
importFrom("graphics", "abline", "axis", "par", "plot", "title")
importFrom("stats", "coef", "coefficients", "kmeans", "lm")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 classes:
'eigen'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 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/SamSPECTRAL/libs/i386/SamSPECTRAL.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/SamSPECTRAL/libs/x64/SamSPECTRAL.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-3.9-bioc/meat/SamSPECTRAL.Rcheck/00check.log'
for details.
SamSPECTRAL.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/SamSPECTRAL_1.38.0.tar.gz && rm -rf SamSPECTRAL.buildbin-libdir && mkdir SamSPECTRAL.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SamSPECTRAL.buildbin-libdir SamSPECTRAL_1.38.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL SamSPECTRAL_1.38.0.zip && rm SamSPECTRAL_1.38.0.tar.gz SamSPECTRAL_1.38.0.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
25 443k 25 112k 0 0 305k 0 0:00:01 --:--:-- 0:00:01 310k
100 443k 100 443k 0 0 1198k 0 --:--:-- --:--:-- --:--:-- 1215k
install for i386
* installing *source* package 'SamSPECTRAL' ...
** 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 Rinit.c -o Rinit.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 conductance_computation.c -o conductance_computation.o
conductance_computation.c: In function 'conductance_computation':
conductance_computation.c:155:17: warning: variable 'repres_ind' set but not used [-Wunused-but-set-variable]
int *density, *repres_ind;
^
conductance_computation.c:155:7: warning: variable 'density' set but not used [-Wunused-but-set-variable]
int *density, *repres_ind;
^
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 maximum_of_rows.c -o maximum_of_rows.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o SamSPECTRAL.dll tmp.def Rinit.o conductance_computation.o maximum_of_rows.o -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/SamSPECTRAL.buildbin-libdir/00LOCK-SamSPECTRAL/00new/SamSPECTRAL/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'SamSPECTRAL'
finding HTML links ... done
Building_Communities html
Civilized_Spectral_Clustering html
Conductance_Calculation html
Connecting html
SamSPECTRAL-package html
SamSPECTRAL html
check.SamSPECTRAL.input html
eigen.values.10 html
eigen.values.1000 html
kneepointDetection html
small html
stmFSC 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 'SamSPECTRAL' ...
** 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 Rinit.c -o Rinit.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 conductance_computation.c -o conductance_computation.o
conductance_computation.c: In function 'conductance_computation':
conductance_computation.c:155:17: warning: variable 'repres_ind' set but not used [-Wunused-but-set-variable]
int *density, *repres_ind;
^
conductance_computation.c:155:7: warning: variable 'density' set but not used [-Wunused-but-set-variable]
int *density, *repres_ind;
^
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 maximum_of_rows.c -o maximum_of_rows.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o SamSPECTRAL.dll tmp.def Rinit.o conductance_computation.o maximum_of_rows.o -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/SamSPECTRAL.buildbin-libdir/SamSPECTRAL/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SamSPECTRAL' as SamSPECTRAL_1.38.0.zip
* DONE (SamSPECTRAL)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'SamSPECTRAL' successfully unpacked and MD5 sums checked
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SamSPECTRAL.Rcheck/examples_i386/SamSPECTRAL-Ex.timings
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SamSPECTRAL.Rcheck/examples_x64/SamSPECTRAL-Ex.timings
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