Daniel Gusenleitner
| Snapshot Date: 2018-02-28 17:01:29 -0500 (Wed, 28 Feb 2018) |
| URL: https://git.bioconductor.org/packages/IrisSpatialFeatures |
| Branch: master |
| Last Commit: 5bc531a |
| Last Changed Date: 2017-10-30 12:54:32 -0500 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-03-01 07:26:08 -0500 (Thu, 01 Mar 2018).
| Package 723/1499 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| IrisSpatialFeatures 1.3.0 Daniel Gusenleitner
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: IrisSpatialFeatures |
| Version: 1.3.0 |
| Command: rm -rf IrisSpatialFeatures.buildbin-libdir IrisSpatialFeatures.Rcheck && mkdir IrisSpatialFeatures.buildbin-libdir IrisSpatialFeatures.Rcheck && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=IrisSpatialFeatures.buildbin-libdir IrisSpatialFeatures_1.3.0.tar.gz >IrisSpatialFeatures.Rcheck\00install.out 2>&1 && cp IrisSpatialFeatures.Rcheck\00install.out IrisSpatialFeatures-install.out && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --library=IrisSpatialFeatures.buildbin-libdir --install="check:IrisSpatialFeatures-install.out" --force-multiarch --no-vignettes --timings IrisSpatialFeatures_1.3.0.tar.gz |
| StartedAt: 2018-03-01 02:08:37 -0500 (Thu, 01 Mar 2018) |
| EndedAt: 2018-03-01 02:22:18 -0500 (Thu, 01 Mar 2018) |
| EllapsedTime: 821.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: IrisSpatialFeatures.Rcheck |
| Warnings: 0 |
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### Running command:
###
### rm -rf IrisSpatialFeatures.buildbin-libdir IrisSpatialFeatures.Rcheck && mkdir IrisSpatialFeatures.buildbin-libdir IrisSpatialFeatures.Rcheck && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=IrisSpatialFeatures.buildbin-libdir IrisSpatialFeatures_1.3.0.tar.gz >IrisSpatialFeatures.Rcheck\00install.out 2>&1 && cp IrisSpatialFeatures.Rcheck\00install.out IrisSpatialFeatures-install.out && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --library=IrisSpatialFeatures.buildbin-libdir --install="check:IrisSpatialFeatures-install.out" --force-multiarch --no-vignettes --timings IrisSpatialFeatures_1.3.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/IrisSpatialFeatures.Rcheck'
* using R Under development (unstable) (2018-01-28 r74175)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'IrisSpatialFeatures/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'IrisSpatialFeatures' version '1.3.0'
* 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 'IrisSpatialFeatures' can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.6Mb
sub-directories of 1Mb or more:
data 1.4Mb
extdata 1.9Mb
libs 1.5Mb
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 ... OK
* 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 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-3.7-bioc/meat/IrisSpatialFeatures.buildbin-libdir/IrisSpatialFeatures/libs/i386/IrisSpatialFeatures.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
threshold_dataset 59.33 0.45 59.78
read_raw 56.67 0.38 57.05
interaction_maps 21.96 7.00 28.97
get_interactions 26.08 0.30 26.39
extract_features 19.75 0.94 20.79
extract_interactions 15.61 0.17 15.78
extract_proximity 12.58 3.06 15.64
get_all_interactions 13.83 0.05 13.88
plot_interactions 13.19 0.01 13.20
extract_nearest_neighbor 7.37 2.65 10.03
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
threshold_dataset 64.58 0.44 65.02
read_raw 57.47 0.34 57.81
interaction_maps 17.76 7.23 25.31
extract_features 17.56 0.61 18.26
extract_proximity 9.82 3.51 13.34
extract_interactions 12.69 0.06 12.75
get_interactions 12.57 0.03 12.61
get_all_interactions 11.61 0.05 11.66
plot_interactions 8.63 0.03 8.65
extract_nearest_neighbor 5.08 2.52 7.60
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.R'
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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.7-bioc/meat/IrisSpatialFeatures.Rcheck/00check.log'
for details.
IrisSpatialFeatures.Rcheck/00install.out
install for i386
* installing *source* package 'IrisSpatialFeatures' ...
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c interaction.cpp -o interaction.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c masking.cpp -o masking.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o IrisSpatialFeatures.dll tmp.def RcppExports.o interaction.o masking.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/IrisSpatialFeatures.buildbin-libdir/IrisSpatialFeatures/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'IrisSpatialFeatures'
finding HTML links ... done
Coordinate-class html
ImageSet-class html
IrisSpatialFeatures-package html
IrisSpatialFeatures_data html
Sample-class html
as.data.frame html
collapse_markers html
extract_ROI html
extract_features html
extract_interactions html
extract_mask html
extract_nearest_neighbor html
extract_proximity html
feature_selection html
get_all_interactions html
get_all_nearest_neighbors html
get_all_proximities html
get_count_ratios html
get_counts_per_mm2 html
get_counts_per_mm2_noncollapsed html
get_interactions html
get_nearest_neighbors html
get_proximities html
interaction_maps html
neighbor_ray_plot html
overview_plot html
plot html
plot_interactions html
plot_nearest_neighbor html
plot_proximities html
raw_data-class html
rayplot_single_coordinate html
read_raw html
threshold_dataset html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'IrisSpatialFeatures' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c interaction.cpp -o interaction.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/local323/include" -O2 -Wall -mtune=generic -c masking.cpp -o masking.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o IrisSpatialFeatures.dll tmp.def RcppExports.o interaction.o masking.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/IrisSpatialFeatures.buildbin-libdir/IrisSpatialFeatures/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'IrisSpatialFeatures' as IrisSpatialFeatures_1.3.0.zip
* DONE (IrisSpatialFeatures)
In R CMD INSTALL
In R CMD INSTALL
|
IrisSpatialFeatures.Rcheck/tests_i386/testthat.Rout
R Under development (unstable) (2018-01-28 r74175) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(IrisSpatialFeatures)
> test_check("IrisSpatialFeatures")
[1] "Sample: MEL2"
[1] "No nuclear map found, skipping .. "
[1] "No nuclear map found, skipping .. "
[1] "Sample: MEL3"
[1] "No nuclear map found, skipping .. "
[1] "No nuclear map found, skipping .. "
== testthat results ===========================================================
OK: 2 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
63.59 0.76 64.32
|
IrisSpatialFeatures.Rcheck/tests_x64/testthat.Rout
R Under development (unstable) (2018-01-28 r74175) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(IrisSpatialFeatures)
> test_check("IrisSpatialFeatures")
[1] "Sample: MEL2"
[1] "No nuclear map found, skipping .. "
[1] "No nuclear map found, skipping .. "
[1] "Sample: MEL3"
[1] "No nuclear map found, skipping .. "
[1] "No nuclear map found, skipping .. "
== testthat results ===========================================================
OK: 2 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
63.82 0.65 64.46
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IrisSpatialFeatures.Rcheck/examples_i386/IrisSpatialFeatures-Ex.timings
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IrisSpatialFeatures.Rcheck/examples_x64/IrisSpatialFeatures-Ex.timings
|