Philipp Angerer
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/destiny |
| Branch: RELEASE_3_10 |
| Last Commit: 1348b8f |
| Last Changed Date: 2020-01-16 06:24:52 -0400 (Thu, 16 Jan 2020) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:25:17 -0400 (Wed, 15 Apr 2020).
| Package 446/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| destiny 3.0.1 Philipp Angerer
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: destiny |
| Version: 3.0.1 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:destiny.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings destiny_3.0.1.tar.gz |
| StartedAt: 2020-04-15 02:39:40 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 02:47:02 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 441.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: destiny.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:destiny.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings destiny_3.0.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/destiny.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '3.0.1'
* 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-3.10-bioc/tmpdir/RtmpczysLq/R.INSTALL25702a362bcc/destiny/man/cube_helix.Rd:53: file link 'hcl.colors' in package 'grDevices' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpczysLq/R.INSTALL25702a362bcc/destiny/man/eig_decomp.Rd:26: file link 'set.seed' in package 'base' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.10-bioc/meat/destiny.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
'tidyr' 'SingleCellExperiment'
A package should be listed in only one of these fields.
'LinkingTo' for 'grDevices' is unused as it has no 'include' directory
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
plot.DPT plot.DiffusionMap
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
get_pca: no visible binding for global variable 'pcs'
plot.DiffusionMap: no visible binding for global variable 'hcl.colors'
plot_differential_map: no visible binding for global variable
'hcl.colors'
plot_gradient_map: no visible binding for global variable 'hcl.colors'
plot_differential_map,DiffusionMap-missing: no visible binding for
global variable 'hcl.colors'
plot_differential_map,GeneRelevance-missing: no visible binding for
global variable 'hcl.colors'
plot_differential_map,matrix-matrix: no visible binding for global
variable 'hcl.colors'
Undefined global functions or variables:
hcl.colors pcs
Consider adding
importFrom("grDevices", "hcl.colors")
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-3.10-bioc/R/library/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)
File 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/destiny/libs/x64/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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
destiny 28.75 0.32 29.21
Gene-Relevance-plotting 6.33 0.25 6.58
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
destiny 11.58 0.26 11.85
Gene-Relevance-plotting 6.39 0.04 6.44
* 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: 1 WARNING, 6 NOTEs
See
'C:/Users/biocbuild/bbs-3.10-bioc/meat/destiny.Rcheck/00check.log'
for details.
destiny.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/destiny_3.0.1.tar.gz && rm -rf destiny.buildbin-libdir && mkdir destiny.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=destiny.buildbin-libdir destiny_3.0.1.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL destiny_3.0.1.zip && rm destiny_3.0.1.tar.gz destiny_3.0.1.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 4220k 100 4220k 0 0 45.7M 0 --:--:-- --:--:-- --:--:-- 47.9M
install for i386
Warning in untar2(tarfile, files, list, exdir, restore_times) :
failed to copy 'destiny/docs/reference/updateObject-methods.html' to 'destiny/docs/reference/updateObject-method.html'
* installing *source* package 'destiny' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/grDevices/include" -I"C:/extsoft/include" -ggdb -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/grDevices/include" -I"C:/extsoft/include" -ggdb -O2 -Wall -mtune=core2 -c censoring.cpp -o censoring.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/grDevices/include" -I"C:/extsoft/include" -ggdb -O2 -Wall -mtune=core2 -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 utils.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/destiny.buildbin-libdir/00LOCK-destiny/00new/destiny/libs/i386
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
From .checkSubclasses(): subclass "dgTMatrix" of class "dsparseMatrix" is not local and is not updated for new inheritance information currently;
[where=<environment: 0x038c78f0>, where2=<environment: namespace:destiny>]
From .checkSubclasses(): subclass "dtTMatrix" of class "dsparseMatrix" is not local and is not updated for new inheritance information currently;
[where=<environment: 0x038c78f0>, where2=<environment: namespace:destiny>]
From .checkSubclasses(): subclass "dsTMatrix" of class "dsparseMatrix" is not local and is not updated for new inheritance information currently;
[where=<environment: 0x038c78f0>, where2=<environment: namespace:destiny>]
From .checkSubclasses(): subclass "dgCMatrix" of class "dsparseMatrix" is not local and is not updated for new inheritance information currently;
[where=<environment: 0x038c78f0>, where2=<environment: namespace:destiny>]
From .checkSubclasses(): subclass "dtCMatrix" of class "dsparseMatrix" is not local and is not updated for new inheritance information currently;
[where=<environment: 0x038c78f0>, where2=<environment: namespace:destiny>]
From .checkSubclasses(): subclass "dsCMatrix" of class "dsparseMatrix" is not local and is not updated for new inheritance information currently;
[where=<environment: 0x038c78f0>, where2=<environment: namespace:destiny>]
From .checkSubclasses(): subclass "dgRMatrix" of class "dsparseMatrix" is not local and is not updated for new inheritance information currently;
[where=<environment: 0x038c78f0>, where2=<environment: namespace:destiny>]
From .checkSubclasses(): subclass "dtRMatrix" of class "dsparseMatrix" is not local and is not updated for new inheritance information currently;
[where=<environment: 0x038c78f0>, where2=<environment: namespace:destiny>]
From .checkSubclasses(): subclass "dsRMatrix" of class "dsparseMatrix" is not local and is not updated for new inheritance information currently;
[where=<environment: 0x038c78f0>, where2=<environment: namespace:destiny>]
** 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
DiffusionMap-methods html
ExpressionSet-helpers html
Gene-Relevance-methods html
Gene-Relevance-plotting html
Gene-Relevance html
Sigmas-class html
coercions html
colorlegend html
cube_helix html
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpczysLq/R.INSTALL25702a362bcc/destiny/man/cube_helix.Rd:53: file link 'hcl.colors' in package 'grDevices' does not exist and so has been treated as a topic
destiny-deprecated html
destiny-generics html
destiny html
dm_predict html
eig_decomp html
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpczysLq/R.INSTALL25702a362bcc/destiny/man/eig_decomp.Rd:26: file link 'set.seed' in package 'base' does not exist and so has been treated as a topic
extractions html
find_dm_k html
find_sigmas html
find_tips html
guo html
knn html
l_which html
plot.DPT html
plot.DiffusionMap html
plot.Sigmas html
projection_dist html
random_root html
updateObject-methods 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
Warning in untar2(tarfile, files, list, exdir, restore_times) :
failed to copy 'destiny/docs/reference/updateObject-methods.html' to 'destiny/docs/reference/updateObject-method.html'
* installing *source* package 'destiny' ...
** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/grDevices/include" -I"C:/extsoft/include" -ggdb -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/grDevices/include" -I"C:/extsoft/include" -ggdb -O2 -Wall -mtune=core2 -c censoring.cpp -o censoring.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/grDevices/include" -I"C:/extsoft/include" -ggdb -O2 -Wall -mtune=core2 -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 utils.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/destiny.buildbin-libdir/destiny/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'destiny' as destiny_3.0.1.zip
* DONE (destiny)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'destiny' successfully unpacked and MD5 sums checked
|
destiny.Rcheck/tests_i386/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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: 67 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
19.70 2.53 22.21
|
destiny.Rcheck/tests_x64/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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: 67 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
17.04 1.71 18.84
|
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destiny.Rcheck/examples_i386/destiny-Ex.timings
|
destiny.Rcheck/examples_x64/destiny-Ex.timings
|