Habil
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/SamSPECTRAL |
| Branch: RELEASE_3_11 |
| Last Commit: 9713378 |
| Last Changed Date: 2020-04-27 14:21:21 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:57:44 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE SamSPECTRAL PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1571/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SamSPECTRAL 1.42.0 Habil
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |
| Package: SamSPECTRAL |
| Version: 1.42.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SamSPECTRAL.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings SamSPECTRAL_1.42.0.tar.gz |
| StartedAt: 2020-10-17 07:56:07 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 07:56:51 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 44.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: SamSPECTRAL.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SamSPECTRAL.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings SamSPECTRAL_1.42.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/SamSPECTRAL.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.42.0'
* 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 '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 '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 png provide title
Consider adding
importFrom("grDevices", "dev.off", "png")
importFrom("graphics", "abline", "axis", "par", "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-3.11-bioc/R/library/SamSPECTRAL/libs/i386/SamSPECTRAL.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.11-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-3.11-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/3.11/bioc/src/contrib/SamSPECTRAL_1.42.0.tar.gz && rm -rf SamSPECTRAL.buildbin-libdir && mkdir SamSPECTRAL.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SamSPECTRAL.buildbin-libdir SamSPECTRAL_1.42.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL SamSPECTRAL_1.42.0.zip && rm SamSPECTRAL_1.42.0.tar.gz SamSPECTRAL_1.42.0.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
100 443k 100 443k 0 0 6958k 0 --:--:-- --:--:-- --:--:-- 7781k
install for i386
* installing *source* package 'SamSPECTRAL' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Rinit.c -o Rinit.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c maximum_of_rows.c -o maximum_of_rows.o
C:/rtools40/mingw32/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-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-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:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Rinit.c -o Rinit.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c maximum_of_rows.c -o maximum_of_rows.o
C:/rtools40/mingw64/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-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/SamSPECTRAL.buildbin-libdir/SamSPECTRAL/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SamSPECTRAL' as SamSPECTRAL_1.42.0.zip
* DONE (SamSPECTRAL)
* installing to library 'C:/Users/biocbuild/bbs-3.11-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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