destiny 2.5.6
Philipp Angerer
| Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/destiny | | Last Changed Rev: 131283 / Revision: 131943 | | Last Changed Date: 2017-07-17 10:32:41 -0400 (Mon, 17 Jul 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings destiny_2.5.6.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/destiny.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘2.5.6’
* 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 ... 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
* 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 ... NOTE
Warning: no function found corresponding to methods exports from ‘destiny’ for: ‘show’
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
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’
Undefined global functions or variables:
Gene
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic 'featureNames' and siglist 'GeneRelevance'
generic 'featureNames<-' and siglist
'GeneRelevance,characterOrFactor'
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 ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'Gene Relevance methods'
‘object’ ‘value’
Objects in \usage without \alias in documentation object 'Gene Relevance methods':
‘\S4method{featureNames}{GeneRelevance}’
‘\S4method{featureNames<-}{GeneRelevance,characterOrFactor}’
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 ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
destiny 8.144 0.131 8.518
Gene-Relevance-plotting 6.090 0.125 6.433
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
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: 2 WARNINGs, 5 NOTEs
See
‘/Users/biocbuild/bbs-3.6-bioc/meat/destiny.Rcheck/00check.log’
for details.
* installing *source* package ‘destiny’ ...
** libs
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/grDevices/include" -I/usr/local/include -ggdb -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/grDevices/include" -I/usr/local/include -ggdb -fPIC -Wall -g -O2 -c censoring.cpp -o censoring.o
censoring.cpp:60:15: warning: variable 'm0' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
} else if (!one_uncertain && one_missing) {
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
censoring.cpp:71:20: note: uninitialized use occurs here
* ( std::erfc((m0-v) / sigma) - std::erfc((m1-v) / sigma) )
^˜
censoring.cpp:60:11: note: remove the 'if' if its condition is always true
} else if (!one_uncertain && one_missing) {
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
censoring.cpp:60:15: warning: variable 'm0' is used uninitialized whenever '&&' condition is false [-Wsometimes-uninitialized]
} else if (!one_uncertain && one_missing) {
^˜˜˜˜˜˜˜˜˜˜˜˜˜
censoring.cpp:71:20: note: uninitialized use occurs here
* ( std::erfc((m0-v) / sigma) - std::erfc((m1-v) / sigma) )
^˜
censoring.cpp:60:15: note: remove the '&&' if its condition is always true
} else if (!one_uncertain && one_missing) {
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
censoring.cpp:55:13: note: initialize the variable 'm0' to silence this warning
double m0, m1;
^
= 0.0
censoring.cpp:60:15: warning: variable 'm1' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
} else if (!one_uncertain && one_missing) {
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
censoring.cpp:71:48: note: uninitialized use occurs here
* ( std::erfc((m0-v) / sigma) - std::erfc((m1-v) / sigma) )
^˜
censoring.cpp:60:11: note: remove the 'if' if its condition is always true
} else if (!one_uncertain && one_missing) {
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
censoring.cpp:60:15: warning: variable 'm1' is used uninitialized whenever '&&' condition is false [-Wsometimes-uninitialized]
} else if (!one_uncertain && one_missing) {
^˜˜˜˜˜˜˜˜˜˜˜˜˜
censoring.cpp:71:48: note: uninitialized use occurs here
* ( std::erfc((m0-v) / sigma) - std::erfc((m1-v) / sigma) )
^˜
censoring.cpp:60:15: note: remove the '&&' if its condition is always true
} else if (!one_uncertain && one_missing) {
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
censoring.cpp:55:17: note: initialize the variable 'm1' to silence this warning
double m0, m1;
^
= 0.0
censoring.cpp:60:15: warning: variable 'use_d' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
} else if (!one_uncertain && one_missing) {
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
censoring.cpp:66:21: note: uninitialized use occurs here
const double v = use_d ? d : c;
^˜˜˜˜
censoring.cpp:60:11: note: remove the 'if' if its condition is always true
} else if (!one_uncertain && one_missing) {
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
censoring.cpp:60:15: warning: variable 'use_d' is used uninitialized whenever '&&' condition is false [-Wsometimes-uninitialized]
} else if (!one_uncertain && one_missing) {
^˜˜˜˜˜˜˜˜˜˜˜˜˜
censoring.cpp:66:21: note: uninitialized use occurs here
const double v = use_d ? d : c;
^˜˜˜˜
censoring.cpp:60:15: note: remove the '&&' if its condition is always true
} else if (!one_uncertain && one_missing) {
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
censoring.cpp:18:12: note: initialize the variable 'use_d' to silence this warning
bool use_d;
^
= false
6 warnings generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/grDevices/include" -I/usr/local/include -ggdb -fPIC -Wall -g -O2 -c no_censoring.cpp -o no_censoring.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o destiny.so RcppExports.o censoring.o no_censoring.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-bioc/meat/destiny.Rcheck/destiny/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (destiny)