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:
###
### rm -rf destiny.buildbin-libdir destiny.Rcheck && mkdir destiny.buildbin-libdir destiny.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=destiny.buildbin-libdir destiny_2.0.9.tar.gz >destiny.Rcheck\00install.out 2>&1 && cp destiny.Rcheck\00install.out destiny-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=destiny.buildbin-libdir --install="check:destiny-install.out" --force-multiarch --no-vignettes --timings destiny_2.0.9.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/destiny.Rcheck'
* using R version 3.3.3 (2017-03-06)
* 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 '2.0.9'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.4-bioc/meat/destiny.buildbin-libdir/destiny/libs/i386/destiny.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'destiny-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: destiny
> ### Title: Create and plot diffusion maps
> ### Aliases: destiny destiny-package
>
> ### ** Examples
>
> demo(destiny, ask = FALSE)
demo(destiny)
---- ˜˜˜˜˜˜˜
> library(destiny)
> data(guo)
> Dark2 <- scales::brewer_pal(palette = 'Dark2')
> palette(Dark2(8L))
> dm_guo <- DiffusionMap(guo, verbose = FALSE,
+ censor_val = 10, censor_range = c(10, 40))
> plot(dm_guo,
+ col = guo$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
** running examples for arch 'x64' ... 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: 2 ERRORs, 9 WARNINGs, 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.4-bioc/meat/destiny.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'destiny' ...
** libs
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include" -I"C:/local323/include" -g -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include" -I"C:/local323/include" -g -O2 -Wall -mtune=core2 -c censoring.cpp -o censoring.o
C:/Rtools/mingw_32/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include" -I"C:/local323/include" -g -O2 -Wall -mtune=core2 -c no_censoring.cpp -o no_censoring.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o destiny.dll tmp.def RcppExports.o censoring.o no_censoring.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.4-bioc/meat/destiny.buildbin-libdir/destiny/libs/i386
** 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
install for x64
* installing *source* package 'destiny' ...
** libs
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include" -I"C:/local323/include" -g -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include" -I"C:/local323/include" -g -O2 -Wall -mtune=core2 -c censoring.cpp -o censoring.o
censoring.cpp: In function 'Rcpp::NumericMatrix predict_censoring_impl(Rcpp::NumericMatrix, Rcpp::NumericMatrix, double, Rcpp::NumericVector, Rcpp::NumericVector, double)':
censoring.cpp:72:17: warning: 'm1' may be used uninitialized in this function [-Wmaybe-uninitialized]
/ sqrt(m1-m0);
^
censoring.cpp:55:15: note: 'm1' was declared here
double m0, m1;
^
censoring.cpp:71:22: warning: 'm0' may be used uninitialized in this function [-Wmaybe-uninitialized]
* ( std::erfc((m0-v) / sigma) - std::erfc((m1-v) / sigma) )
^
censoring.cpp:55:11: note: 'm0' was declared here
double m0, m1;
^
censoring.cpp:66:33: warning: 'use_d' may be used uninitialized in this function [-Wmaybe-uninitialized]
const double v = use_d ? d : c;
^
censoring.cpp:18:7: note: 'use_d' was declared here
bool use_d;
^
censoring.cpp: In function 'Eigen::SparseMatrix<double, 0, int> censoring_impl(Rcpp::NumericMatrix, SEXP, SEXP, SEXP, Rcpp::NumericVector, SEXP, Rcpp::Function)':
censoring.cpp:72:17: warning: 'm1' may be used uninitialized in this function [-Wmaybe-uninitialized]
/ sqrt(m1-m0);
^
censoring.cpp:55:15: note: 'm1' was declared here
double m0, m1;
^
censoring.cpp:71:22: warning: 'm0' may be used uninitialized in this function [-Wmaybe-uninitialized]
* ( std::erfc((m0-v) / sigma) - std::erfc((m1-v) / sigma) )
^
censoring.cpp:55:11: note: 'm0' was declared here
double m0, m1;
^
censoring.cpp:66:33: warning: 'use_d' may be used uninitialized in this function [-Wmaybe-uninitialized]
const double v = use_d ? d : c;
^
censoring.cpp:18:7: note: 'use_d' was declared here
bool use_d;
^
C:/Rtools/mingw_64/bin/g++ -std=c++0x -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/RcppEigen/include" -I"C:/local323/include" -g -O2 -Wall -mtune=core2 -c no_censoring.cpp -o no_censoring.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o destiny.dll tmp.def RcppExports.o censoring.o no_censoring.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.4-bioc/meat/destiny.buildbin-libdir/destiny/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'destiny' as destiny_2.0.9.zip
* DONE (destiny)