Philipp Angerer
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/destiny |
| Branch: RELEASE_3_6 |
| Last Commit: 24459aa |
| Last Changed Date: 2018-02-27 11:41:49 -0400 (Tue, 27 Feb 2018) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:26:39 -0400 (Thu, 12 Apr 2018).
| Package 358/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| destiny 2.6.2 Philipp Angerer
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: destiny |
| Version: 2.6.2 |
| Command: rm -rf destiny.buildbin-libdir destiny.Rcheck && mkdir destiny.buildbin-libdir destiny.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=destiny.buildbin-libdir destiny_2.6.2.tar.gz >destiny.Rcheck\00install.out 2>&1 && cp destiny.Rcheck\00install.out destiny-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=destiny.buildbin-libdir --install="check:destiny-install.out" --force-multiarch --no-vignettes --timings destiny_2.6.2.tar.gz |
| StartedAt: 2018-04-11 23:28:39 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 23:34:18 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 338.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: destiny.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### rm -rf destiny.buildbin-libdir destiny.Rcheck && mkdir destiny.buildbin-libdir destiny.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=destiny.buildbin-libdir destiny_2.6.2.tar.gz >destiny.Rcheck\00install.out 2>&1 && cp destiny.Rcheck\00install.out destiny-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=destiny.buildbin-libdir --install="check:destiny-install.out" --force-multiarch --no-vignettes --timings destiny_2.6.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/destiny.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'destiny/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'destiny' version '2.6.2'
* package encoding: UTF-8
* 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 'destiny' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0ARBDW/R.INSTALL1ba4435c1236/destiny/man/DiffusionMap-class.Rd:56: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0ARBDW/R.INSTALL1ba4435c1236/destiny/man/ExpressionSet-helpers.Rd:10: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0ARBDW/R.INSTALL1ba4435c1236/destiny/man/ExpressionSet-helpers.Rd:34: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0ARBDW/R.INSTALL1ba4435c1236/destiny/man/ExpressionSet-helpers.Rd:20: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0ARBDW/R.INSTALL1ba4435c1236/destiny/man/ExpressionSet-helpers.Rd:31: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0ARBDW/R.INSTALL1ba4435c1236/destiny/man/ExpressionSet-helpers.Rd:50: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0ARBDW/R.INSTALL1ba4435c1236/destiny/man/dm_predict.Rd:13: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0ARBDW/R.INSTALL1ba4435c1236/destiny/man/find_sigmas.Rd:13: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0ARBDW/R.INSTALL1ba4435c1236/destiny/man/guo.Rd:10: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0ARBDW/R.INSTALL1ba4435c1236/destiny/man/guo.Rd:16: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0ARBDW/R.INSTALL1ba4435c1236/destiny/man/projection_dist.Rd:17: missing file link 'ExpressionSet'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/destiny.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 5.5Mb
sub-directories of 1Mb or more:
doc 3.1Mb
libs 1.7Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
'LinkingTo' for 'grDevices' is unused as it has no 'include' directory
* 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
Namespace in Imports field not imported from: 'scatterplot3d'
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plot_gradient_map_impl : <anonymous>: no visible binding for global
variable 'Gene'
scatterplot3d : <anonymous>: no visible global function definition for
'formula'
scatterplot3d : <anonymous>: no visible global function definition for
'predict'
Undefined global functions or variables:
Gene formula predict
Consider adding
importFrom("stats", "formula", "predict")
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 ... NOTE
S3 methods shown with full name in documentation object 'plot.DPT':
'plot.DPT'
S3 methods shown with full name in documentation object 'plot.DiffusionMap':
'plot.DiffusionMap'
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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-3.6-bioc/meat/destiny.buildbin-libdir/destiny/libs/i386/destiny.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
destiny 28.93 0.20 29.17
Gene-Relevance-plotting 7.08 0.19 7.27
DiffusionMap-class 5.14 0.30 5.43
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
destiny 13.20 0.10 13.31
Gene-Relevance-plotting 7.14 0.15 7.29
* 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 ... NOTE
'::' or ':::' import not declared from: 'viridis'
'library' or 'require' calls not declared from:
'IRdisplay' 'IRkernel' 'base64enc' 'repr' 'xlsx'
* 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, 7 NOTEs
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/destiny.Rcheck/00check.log'
for details.
destiny.Rcheck/00install.out
install for i386
* installing *source* package 'destiny' ...
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/grDevices/include" -I"C:/local323/include" -ggdb -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/grDevices/include" -I"C:/local323/include" -ggdb -O2 -Wall -mtune=generic -c censoring.cpp -o censoring.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/grDevices/include" -I"C:/local323/include" -ggdb -O2 -Wall -mtune=generic -c knn.cpp -o knn.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/grDevices/include" -I"C:/local323/include" -ggdb -O2 -Wall -mtune=generic -c utils.cpp -o utils.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o destiny.dll tmp.def RcppExports.o censoring.o knn.o utils.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/destiny.buildbin-libdir/destiny/libs/i386
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'destiny'
finding HTML links ... done
DPT-matrix-methods html
DPT-methods html
DPT html
DiffusionMap-accessors html
DiffusionMap-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0ARBDW/R.INSTALL1ba4435c1236/destiny/man/DiffusionMap-class.Rd:56: missing file link 'ExpressionSet'
DiffusionMap-methods html
ExpressionSet-helpers html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0ARBDW/R.INSTALL1ba4435c1236/destiny/man/ExpressionSet-helpers.Rd:10: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0ARBDW/R.INSTALL1ba4435c1236/destiny/man/ExpressionSet-helpers.Rd:34: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0ARBDW/R.INSTALL1ba4435c1236/destiny/man/ExpressionSet-helpers.Rd:20: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0ARBDW/R.INSTALL1ba4435c1236/destiny/man/ExpressionSet-helpers.Rd:31: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0ARBDW/R.INSTALL1ba4435c1236/destiny/man/ExpressionSet-helpers.Rd:50: missing file link 'ExpressionSet'
Gene-Relevance-methods html
Gene-Relevance-plotting html
Gene-Relevance html
Sigmas-class html
coercions html
colorlegend html
cube_helix html
destiny-deprecated html
destiny-generics html
destiny html
dm_predict html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0ARBDW/R.INSTALL1ba4435c1236/destiny/man/dm_predict.Rd:13: missing file link 'ExpressionSet'
eig_decomp html
extractions html
find_dm_k html
find_sigmas html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0ARBDW/R.INSTALL1ba4435c1236/destiny/man/find_sigmas.Rd:13: missing file link 'ExpressionSet'
find_tips html
guo html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0ARBDW/R.INSTALL1ba4435c1236/destiny/man/guo.Rd:10: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0ARBDW/R.INSTALL1ba4435c1236/destiny/man/guo.Rd:16: missing file link 'ExpressionSet'
knn html
l_which html
plot.DPT html
plot.DiffusionMap html
plot.Sigmas html
projection_dist html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0ARBDW/R.INSTALL1ba4435c1236/destiny/man/projection_dist.Rd:17: missing file link 'ExpressionSet'
random_root html
updateObject-method html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'destiny' ...
** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/grDevices/include" -I"C:/local323/include" -ggdb -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/grDevices/include" -I"C:/local323/include" -ggdb -O2 -Wall -mtune=generic -c censoring.cpp -o censoring.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/grDevices/include" -I"C:/local323/include" -ggdb -O2 -Wall -mtune=generic -c knn.cpp -o knn.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/grDevices/include" -I"C:/local323/include" -ggdb -O2 -Wall -mtune=generic -c utils.cpp -o utils.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o destiny.dll tmp.def RcppExports.o censoring.o knn.o utils.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/destiny.buildbin-libdir/destiny/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'destiny' as destiny_2.6.2.zip
* DONE (destiny)
In R CMD INSTALL
In R CMD INSTALL
|
destiny.Rcheck/tests_i386/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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(destiny)
>
> test_check('destiny')
== testthat results ===========================================================
OK: 10 SKIPPED: 1 FAILED: 0
>
> proc.time()
user system elapsed
6.68 0.31 7.10
|
destiny.Rcheck/tests_x64/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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(destiny)
>
> test_check('destiny')
== testthat results ===========================================================
OK: 10 SKIPPED: 1 FAILED: 0
>
> proc.time()
user system elapsed
8.17 0.35 8.56
|
|
destiny.Rcheck/examples_i386/destiny-Ex.timings
|
destiny.Rcheck/examples_x64/destiny-Ex.timings
|