cytofkit 1.6.5
Jinmiao Chen , Hao Chen
| 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/cytofkit | | Last Changed Rev: 127717 / Revision: 128728 | | Last Changed Date: 2017-03-26 21:54:19 -0400 (Sun, 26 Mar 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ WARNINGS ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
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### Running command:
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### rm -rf cytofkit.buildbin-libdir cytofkit.Rcheck && mkdir cytofkit.buildbin-libdir cytofkit.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cytofkit.buildbin-libdir cytofkit_1.6.5.tar.gz >cytofkit.Rcheck\00install.out 2>&1 && cp cytofkit.Rcheck\00install.out cytofkit-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=cytofkit.buildbin-libdir --install="check:cytofkit-install.out" --force-multiarch --no-vignettes --timings cytofkit_1.6.5.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/cytofkit.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 'cytofkit/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'cytofkit' version '1.6.5'
* 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 'cytofkit' can be installed ... OK
* checking installed package size ... NOTE
installed size is 7.4Mb
sub-directories of 1Mb or more:
doc 1.7Mb
extdata 4.0Mb
libs 1.4Mb
* 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 ...Loading required package: ggplot2
Loading required package: plyr
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 'cytofkit'
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 'cytofkit'
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 loading without being on the library search path ... WARNING
Loading required package: ggplot2
Loading required package: plyr
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 'cytofkit'
Execution halted
It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ...Loading required package: ggplot2
Loading required package: plyr
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 'cytofkit'
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 'cytofkit'
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 loading without being on the library search path ... WARNING
Loading required package: ggplot2
Loading required package: plyr
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 'cytofkit'
Execution halted
It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
* checking dependencies in R code ... NOTE
Error: package or namespace load failed for 'cytofkit'
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 ... OK
* 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 ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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-3.4-bioc/meat/cytofkit.buildbin-libdir/cytofkit/libs/i386/cytofkit.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' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
cytof_progression 9.88 0.66 15.7
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
cytof_progression 12.04 0.34 22.72
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
Running 'runTests.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: 6 WARNINGs, 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.4-bioc/meat/cytofkit.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'cytofkit' ...
** libs
C:/Rtools/mingw_32/bin/g++ -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:/local323/include" -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -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:/local323/include" -O2 -Wall -mtune=core2 -c jaccard_coeff.cpp -o jaccard_coeff.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o cytofkit.dll tmp.def RcppExports.o jaccard_coeff.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/cytofkit.buildbin-libdir/cytofkit/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'cytofkit' ...
** libs
C:/Rtools/mingw_64/bin/g++ -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:/local323/include" -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -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:/local323/include" -O2 -Wall -mtune=core2 -c jaccard_coeff.cpp -o jaccard_coeff.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o cytofkit.dll tmp.def RcppExports.o jaccard_coeff.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/cytofkit.buildbin-libdir/cytofkit/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cytofkit' as cytofkit_1.6.5.zip
* DONE (cytofkit)