destiny 2.0.9
Philipp Angerer
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/destiny | | Last Changed Rev: 128063 / Revision: 128728 | | Last Changed Date: 2017-04-05 04:33:42 -0400 (Wed, 05 Apr 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ ERROR ] | | |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | ERROR | OK | |
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### Running command:
###
### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings destiny_2.0.9.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/destiny.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘destiny/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘destiny’ version ‘2.0.9’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘destiny’ can be installed ... OK
* checking installed package size ... OK
* 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
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ...Error : .onLoad failed in loadNamespace() for 'destiny', details:
call: set_palette(gud_default_palette)
error: could not find function "getFromNamespace"
Error: package or namespace load failed for ‘destiny’
Execution halted
It looks like this package (or one of its dependent packages) has an
unstated dependence on a standard package. All dependencies must be
declared in DESCRIPTION.
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
* checking whether the package can be unloaded cleanly ... WARNING
Error : .onLoad failed in loadNamespace() for 'destiny', details:
call: set_palette(gud_default_palette)
error: could not find function "getFromNamespace"
Error: package or namespace load failed for ‘destiny’
Execution halted
* checking whether the namespace can be loaded with stated dependencies ... WARNING
Error: .onLoad failed in loadNamespace() for 'destiny', details:
call: set_palette(gud_default_palette)
error: could not find function "getFromNamespace"
Execution halted
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Error: package or namespace load failed for ‘destiny’
Call sequence:
2: stop(gettextf("package or namespace load failed for %s", sQuote(package)),
call. = FALSE, domain = NA)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... WARNING
Foreign function call to a base package:
.Call(getFromNamespace("C_palette", "grDevices"), ...)
Packages should not make .C/.Call/.External/.Fortran calls to a base
package. They are not part of the API, for use only by R itself and
subject to change without notice.
* checking R code for possible problems ... NOTE
Error: .onLoad failed in loadNamespace() for 'destiny', details:
call: set_palette(gud_default_palette)
error: could not find function "getFromNamespace"
Execution halted
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic '[' and siglist 'DPT,index,index,logicalOrMissing'
generic '[' and siglist 'DPT,index,missing,logicalOrMissing'
generic '[' and siglist 'DPT,missing,index,logicalOrMissing'
generic '[' and siglist 'DPT,missing,missing,logicalOrMissing'
generic '[[' and siglist 'DPT,index,index'
generic 'dim' and siglist 'DPT'
generic 'ncol' and siglist 'DPT'
generic 'nrow' and siglist 'DPT'
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 ... WARNING
Codoc mismatches from documentation object 'DiffusionMap class':
DiffusionMap
Code: function(data, sigma = "local", k = find_dm_k(n_samples(data) -
1L), n_eigs = min(20L, n_samples(data) - 2L),
density_norm = TRUE, ..., distance = c("euclidean",
"cosine", "rankcor"), n_local = 5L, censor_val = NULL,
censor_range = NULL, missing_range = NULL, vars =
NULL, verbose = !is.null(censor_range), suppress_dpt =
FALSE)
Docs: function(data, sigma = "local", k = find_dm_k(nrow(data) - 1L),
n_eigs = min(20L, nrow(data) - 2L), density_norm =
TRUE, ..., distance = c("euclidean", "cosine",
"rankcor"), n_local = 5L, censor_val = NULL,
censor_range = NULL, missing_range = NULL, vars =
NULL, verbose = !is.null(censor_range), suppress_dpt =
FALSE)
Mismatches in argument default values:
Name: 'k' Code: find_dm_k(n_samples(data) - 1L) Docs: find_dm_k(nrow(data) - 1L)
Name: 'n_eigs' Code: min(20L, n_samples(data) - 2L) Docs: min(20L, nrow(data) - 2L)
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'DPT matrix methods'
‘x’ ‘i’ ‘j’ ‘...’ ‘drop’
Objects in \usage without \alias in documentation object 'DPT matrix methods':
‘\S4method{[}{DPT,index,index,logicalOrMissing}’
‘\S4method{[}{DPT,index,missing,logicalOrMissing}’
‘\S4method{[}{DPT,missing,index,logicalOrMissing}’
‘\S4method{[}{DPT,missing,missing,logicalOrMissing}’
‘\S4method{nrow}{DPT}’ ‘\S4method{ncol}{DPT}’ ‘\S4method{dim}{DPT}’
Objects in \usage without \alias in documentation object 'extractions':
‘\S4method{[[}{DPT,index,index}’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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 ... WARNING
Non-portable flags in variable 'PKG_CXXFLAGS':
-g
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘destiny-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: destiny
> ### Title: Create and plot diffusion maps
> ### Aliases: destiny destiny-package
>
> ### ** Examples
>
> demo(destiny, ask = FALSE)
demo(destiny)
---- ˜˜˜˜˜˜˜
> library(destiny)
> data(guo)
> Dark2 <- scales::brewer_pal(palette = 'Dark2')
> palette(Dark2(8L))
> dm_guo <- DiffusionMap(guo, verbose = FALSE,
+ censor_val = 10, censor_range = c(10, 40))
> plot(dm_guo,
+ col = guo$num_cells, pch = 20)
Error in mtext(lab, side = side, line = line, at = at, col = col.lab, :
object 'linepad' not found
Calls: demo ... plot.DiffusionMap -> scatterplot3d -> mytext2 -> mtext
Execution halted
* 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 ERROR, 7 WARNINGs, 3 NOTEs
See
‘/home/biocbuild/bbs-3.4-bioc/meat/destiny.Rcheck/00check.log’
for details.
* installing *source* package ‘destiny’ ...
** libs
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include" -g -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
In file included from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/Core:276:0,
from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/Dense:1,
from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigenForward.h:30,
from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
from RcppExports.cpp:4:
/home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/src/Core/Functors.h:973:28: warning: ‘template<class _Operation> class std::binder2nd’ is deprecated [-Wdeprecated-declarations]
struct functor_traits<std::binder2nd<T> >
^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
from /usr/include/c++/5/string:48,
from /usr/include/c++/5/bits/locale_classes.h:40,
from /usr/include/c++/5/bits/ios_base.h:41,
from /usr/include/c++/5/ios:42,
from /usr/include/c++/5/ostream:38,
from /usr/include/c++/5/iterator:64,
from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigenForward.h:25,
from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
from RcppExports.cpp:4:
/usr/include/c++/5/backward/binders.h:143:11: note: declared here
class binder2nd
^
In file included from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/Core:276:0,
from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/Dense:1,
from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigenForward.h:30,
from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
from RcppExports.cpp:4:
/home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/src/Core/Functors.h:977:28: warning: ‘template<class _Operation> class std::binder1st’ is deprecated [-Wdeprecated-declarations]
struct functor_traits<std::binder1st<T> >
^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
from /usr/include/c++/5/string:48,
from /usr/include/c++/5/bits/locale_classes.h:40,
from /usr/include/c++/5/bits/ios_base.h:41,
from /usr/include/c++/5/ios:42,
from /usr/include/c++/5/ostream:38,
from /usr/include/c++/5/iterator:64,
from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigenForward.h:25,
from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
from RcppExports.cpp:4:
/usr/include/c++/5/backward/binders.h:108:11: note: declared here
class binder1st
^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include" -g -fpic -g -O2 -c censoring.cpp -o censoring.o
In file included from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/Core:276:0,
from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/Dense:1,
from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigenForward.h:30,
from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
from censoring.cpp:7:
/home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/src/Core/Functors.h:973:28: warning: ‘template<class _Operation> class std::binder2nd’ is deprecated [-Wdeprecated-declarations]
struct functor_traits<std::binder2nd<T> >
^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
from /usr/include/c++/5/string:48,
from /usr/include/c++/5/stdexcept:39,
from /usr/include/c++/5/array:38,
from /usr/include/c++/5/tuple:39,
from /usr/include/c++/5/unordered_map:41,
from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp/platform/compiler.h:153,
from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:48,
from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:29,
from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
from censoring.cpp:6:
/usr/include/c++/5/backward/binders.h:143:11: note: declared here
class binder2nd
^
In file included from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/Core:276:0,
from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/Dense:1,
from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigenForward.h:30,
from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
from censoring.cpp:7:
/home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/src/Core/Functors.h:977:28: warning: ‘template<class _Operation> class std::binder1st’ is deprecated [-Wdeprecated-declarations]
struct functor_traits<std::binder1st<T> >
^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
from /usr/include/c++/5/string:48,
from /usr/include/c++/5/stdexcept:39,
from /usr/include/c++/5/array:38,
from /usr/include/c++/5/tuple:39,
from /usr/include/c++/5/unordered_map:41,
from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp/platform/compiler.h:153,
from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:48,
from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:29,
from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
from censoring.cpp:6:
/usr/include/c++/5/backward/binders.h:108:11: note: declared here
class binder1st
^
g++ -std=c++11 -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include" -g -fpic -g -O2 -c no_censoring.cpp -o no_censoring.o
In file included from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/Core:276:0,
from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/Dense:1,
from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigenForward.h:30,
from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
from no_censoring.cpp:5:
/home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/src/Core/Functors.h:973:28: warning: ‘template<class _Operation> class std::binder2nd’ is deprecated [-Wdeprecated-declarations]
struct functor_traits<std::binder2nd<T> >
^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
from /usr/include/c++/5/string:48,
from /usr/include/c++/5/stdexcept:39,
from /usr/include/c++/5/array:38,
from /usr/include/c++/5/tuple:39,
from /usr/include/c++/5/unordered_map:41,
from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp/platform/compiler.h:153,
from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:48,
from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:29,
from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
from no_censoring.cpp:4:
/usr/include/c++/5/backward/binders.h:143:11: note: declared here
class binder2nd
^
In file included from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/Core:276:0,
from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/Dense:1,
from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigenForward.h:30,
from /home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
from no_censoring.cpp:5:
/home/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include/Eigen/src/Core/Functors.h:977:28: warning: ‘template<class _Operation> class std::binder1st’ is deprecated [-Wdeprecated-declarations]
struct functor_traits<std::binder1st<T> >
^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
from /usr/include/c++/5/string:48,
from /usr/include/c++/5/stdexcept:39,
from /usr/include/c++/5/array:38,
from /usr/include/c++/5/tuple:39,
from /usr/include/c++/5/unordered_map:41,
from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp/platform/compiler.h:153,
from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:48,
from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/RcppCommon.h:29,
from /home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include/Rcpp.h:27,
from no_censoring.cpp:4:
/usr/include/c++/5/backward/binders.h:108:11: note: declared here
class binder1st
^
g++ -std=c++11 -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o destiny.so RcppExports.o censoring.o no_censoring.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/destiny.Rcheck/destiny/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
Creating a generic function for ‘nrow’ from package ‘base’ in package ‘destiny’
Creating a generic function for ‘ncol’ from package ‘base’ in package ‘destiny’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (destiny)