Version: 0.4.3
checking re-building of vignette outputs ... WARNING ``` Error in re-building vignettes: ... ! File ended while scanning use of \@@BOOKMARK. \par l.107 \begin{document}
pandoc: Error producing PDF from TeX source Error: processing vignette 'model-calibration.Rmd' failed with diagnostics: pandoc document conversion failed with error 43 Execution halted ```
Version: 0.6.0
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: > > test_check("condformat") Unable to find any JVMs matching version "(null)". No Java runtime present, try --request to install.
testthat results ================================================================ OK: 53 SKIPPED: 0 FAILED: 1 1. Error: condformat2excel generates a file (@test_rendering.R#22)
Error: testthat unit tests failed Execution halted ```
checking dependencies in R code ... NOTE
Unable to find any JVMs matching version "(null)".
No Java runtime present, try --request to install.
Unable to find any JVMs matching version "(null)".
No Java runtime present, try --request to install.
Namespace in Imports field not imported from: ‘utils’
All declared Imports should be used.
Version: 0.2.3
Installation failed.
See ‘/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/checks/cpr/new/cpr.Rcheck/00install.out’ for details.
* installing *source* package ‘cpr’ ...
** package ‘cpr’ successfully unpacked and MD5 sums checked
** libs
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/RcppArmadillo/include" -I/usr/local/include -I../inst/include -DARMA_64BIT_WORD -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/RcppArmadillo/include" -I/usr/local/include -I../inst/include -DARMA_64BIT_WORD -fPIC -Wall -g -O2 -c boehm.cpp -o boehm.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/RcppArmadillo/include" -I/usr/local/include -I../inst/include -DARMA_64BIT_WORD -fPIC -Wall -g -O2 -c bsplines.cpp -o bsplines.o
bsplines.cpp:24:10: warning: unused variable 'a' [-Wunused-variable]
double a = 0.0;
^
bsplines.cpp:25:10: warning: unused variable 'b' [-Wunused-variable]
double b = 0.0;
^
2 warnings generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/RcppArmadillo/include" -I/usr/local/include -I../inst/include -DARMA_64BIT_WORD -fPIC -Wall -g -O2 -c cpr.cpp -o cpr.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/RcppArmadillo/include" -I/usr/local/include -I../inst/include -DARMA_64BIT_WORD -fPIC -Wall -g -O2 -c diag_only.cpp -o diag_only.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/RcppArmadillo/include" -I/usr/local/include -I../inst/include -DARMA_64BIT_WORD -fPIC -Wall -g -O2 -c matrix_rank.cpp -o matrix_rank.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/RcppArmadillo/include" -I/usr/local/include -fPIC -Wall -pedantic -O0 -c registerDynamicSymbol.c -o registerDynamicSymbol.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/RcppArmadillo/include" -I/usr/local/include -I../inst/include -DARMA_64BIT_WORD -fPIC -Wall -g -O2 -c tensors.cpp -o tensors.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 cpr.so RcppExports.o boehm.o bsplines.o cpr.o diag_only.o matrix_rank.o registerDynamicSymbol.o tensors.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
ld: library not found for -lquadmath
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [cpr.so] Error 1
ERROR: compilation failed for package ‘cpr’
* removing ‘/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/checks/cpr/new/cpr.Rcheck/cpr’
* installing *source* package ‘cpr’ ...
** package ‘cpr’ successfully unpacked and MD5 sums checked
** libs
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/RcppArmadillo/include" -I/usr/local/include -I../inst/include -DARMA_64BIT_WORD -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/RcppArmadillo/include" -I/usr/local/include -I../inst/include -DARMA_64BIT_WORD -fPIC -Wall -g -O2 -c boehm.cpp -o boehm.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/RcppArmadillo/include" -I/usr/local/include -I../inst/include -DARMA_64BIT_WORD -fPIC -Wall -g -O2 -c bsplines.cpp -o bsplines.o
bsplines.cpp:24:10: warning: unused variable 'a' [-Wunused-variable]
double a = 0.0;
^
bsplines.cpp:25:10: warning: unused variable 'b' [-Wunused-variable]
double b = 0.0;
^
2 warnings generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/RcppArmadillo/include" -I/usr/local/include -I../inst/include -DARMA_64BIT_WORD -fPIC -Wall -g -O2 -c cpr.cpp -o cpr.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/RcppArmadillo/include" -I/usr/local/include -I../inst/include -DARMA_64BIT_WORD -fPIC -Wall -g -O2 -c diag_only.cpp -o diag_only.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/RcppArmadillo/include" -I/usr/local/include -I../inst/include -DARMA_64BIT_WORD -fPIC -Wall -g -O2 -c matrix_rank.cpp -o matrix_rank.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/RcppArmadillo/include" -I/usr/local/include -fPIC -Wall -pedantic -O0 -c registerDynamicSymbol.c -o registerDynamicSymbol.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/cpr/RcppArmadillo/include" -I/usr/local/include -I../inst/include -DARMA_64BIT_WORD -fPIC -Wall -g -O2 -c tensors.cpp -o tensors.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 cpr.so RcppExports.o boehm.o bsplines.o cpr.o diag_only.o matrix_rank.o registerDynamicSymbol.o tensors.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
ld: library not found for -lquadmath
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [cpr.so] Error 1
ERROR: compilation failed for package ‘cpr’
* removing ‘/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/checks/cpr/old/cpr.Rcheck/cpr’
Version: 2.2.8
Namespace in Imports field not imported from: ‘Rcpp’
All declared Imports should be used.
Version: 0.1.6
checking examples ... ERROR ``` ...
mutate_each()
is deprecated.
Use mutate_all()
, mutate_at()
or mutate_if()
instead.
To map funs
over a selection of variables, use mutate_at()
response_window <- subset_by_window(data, window_start_time = 15500, window_end_time = 21000,
response_time <- make_time_sequence_data(response_window, time_bin_size = 500, aois = "Animate",
time_cluster_data <- make_time_cluster_data(data = response_time, predictor_column = "SexM",
checking tests ...
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
Computing t.test for each time bin...
Computing t.test for each time bin...
`mutate_each()` is deprecated.
Use `mutate_all()`, `mutate_at()` or `mutate_if()` instead.
To map `funs` over a selection of variables, use `mutate_at()`
Avg. window length in new data will be 5500
Performing Trackloss Analysis...
Will exclude trials whose trackloss proportion is greater than : 0.25
...removed 33 trials.
Error in UseMethod("make_time_cluster_data") :
no applicable method for 'make_time_cluster_data' applied to an object of class "data.frame"
Calls: test_check ... source_file -> eval -> eval -> make_time_cluster_data
testthat results ================================================================
OK: 38 SKIPPED: 0 FAILED: 0
Execution halted
Version: 0.3.0
Namespace in Imports field not imported from: ‘magrittr’
All declared Imports should be used.
Version: 0.4.4
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: testthat results ================================================================ OK: 49 SKIPPED: 0 FAILED: 10
Error: testthat unit tests failed Execution halted ```
Version: 0.0.2
Namespaces in Imports field not imported from:
‘ggplot2’ ‘maptools’ ‘rgeos’ ‘stringr’ ‘tidyr’
All declared Imports should be used.
Version: 1.0.5
checking R code for possible problems ... NOTE
default_fields.character: no visible binding for global variable
‘defaults’
Undefined global functions or variables:
defaults
checking Rd \usage sections ... NOTE ``` S3 methods shown with full name in documentation object 'as.data.frame.GDCResults': ‘as.data.frame.GDCResults’
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. ```
Version: 0.1.1
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output:
testthat results ================================================================ OK: 3 SKIPPED: 0 FAILED: 2 1. Error: query returns a list of data.frames (@test_query.R#4) 2. Error: no problems if no results (@test_query.R#26)
Error: testthat unit tests failed Execution halted ```
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
Quitting from lines 34-37 (geoparser.Rmd)
Error: processing vignette 'geoparser.Rmd' failed with diagnostics:
HTTP failure: 401
Execution halted
Version: 0.1.1
Namespaces in Imports field not imported from:
‘gridExtra’ ‘lazyeval’ ‘readr’
All declared Imports should be used.
Version: 2.2.1
Namespace in Imports field not imported from: ‘reshape2’
All declared Imports should be used.
Version: 1.0
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: > > if (Sys.getenv("NOT_CRAN") == "true") { # like global skip_on_cran
Initial plotError in file(filename, "r", encoding = encoding) : cannot open the connection Calls: test_check ... source -> withVisible -> eval -> eval -> source -> file In addition: Warning message: In file(filename, "r", encoding = encoding) : cannot open file '../../inst/ggraptR/functions/helper.R': No such file or directory testthat results ================================================================ OK: 0 SKIPPED: 0 FAILED: 0 Execution halted ```
checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘DBI’ ‘GGally’ ‘RColorBrewer’ ‘Rcpp’ ‘assertthat’ ‘backports’
‘colorspace’ ‘colourpicker’ ‘evaluate’ ‘futile.options’ ‘gdtools’
‘gtable’ ‘htmltools’ ‘htmlwidgets’ ‘httpuv’ ‘labeling’ ‘lambda.r’
‘lazyeval’ ‘magrittr’ ‘miniUI’ ‘munsell’ ‘plyr’ ‘reshape’ ‘rprojroot’
‘scales’ ‘stringi’ ‘stringr’ ‘svglite’ ‘tibble’ ‘xtable’ ‘yaml’
All declared Imports should be used.
Version: 0.3
Namespace in Imports field not imported from: ‘lazyeval’
All declared Imports should be used.
Version: 0.4.3
Package unavailable to check Rd xrefs: ‘plyr’
Version: 1.5.1.2
Package suggested but not available for checking: ‘taxstats’
Version: 0.1.3
Note: found 13617 marked UTF-8 strings
Version: 0.2.2
Namespace in Imports field not imported from: ‘ggplot2’
All declared Imports should be used.
Version: 1.2.0
Version: 0.0.1
Package suggested but not available for checking: ‘hurricaneexposuredata’
Version: 1.0.0
Package unavailable to check Rd xrefs: ‘xtable’
Version: 1.0.0
Installation failed.
See ‘/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/checks/jqr/new/jqr.Rcheck/00install.out’ for details.
* installing *source* package ‘jqr’ ...
** package ‘jqr’ successfully unpacked and MD5 sums checked
Using PKG_CFLAGS=-I/usr/local/opt/jq/include
Using PKG_LIBS=-L/usr/local/lib -ljq
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libjq was not found.
On Ubuntu 14.04 or 16.04 you can use the PPA:
sudo add-apt-repository -y ppa:opencpu/jq
sudo apt-get update
sudo apt-get install libjq-dev
On other sytems try installing:
* deb: libjq-dev (Debian, Ubuntu 16.10 and up).
* rpm: jq-devel (Fedora, EPEL)
* csw: libjq_dev (Solaris)
* brew: jq (OSX)
If is already installed set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘jqr’
* removing ‘/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/checks/jqr/new/jqr.Rcheck/jqr’
* installing *source* package ‘jqr’ ...
** package ‘jqr’ successfully unpacked and MD5 sums checked
Using PKG_CFLAGS=-I/usr/local/opt/jq/include
Using PKG_LIBS=-L/usr/local/lib -ljq
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libjq was not found.
On Ubuntu 14.04 or 16.04 you can use the PPA:
sudo add-apt-repository -y ppa:opencpu/jq
sudo apt-get update
sudo apt-get install libjq-dev
On other sytems try installing:
* deb: libjq-dev (Debian, Ubuntu 16.10 and up).
* rpm: jq-devel (Fedora, EPEL)
* csw: libjq_dev (Solaris)
* brew: jq (OSX)
If is already installed set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘jqr’
* removing ‘/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/checks/jqr/old/jqr.Rcheck/jqr’
Version: 1.3.1
Namespaces in Imports field not imported from:
‘Rcpp’ ‘memoise’
All declared Imports should be used.
Version: 1.0.1
amendColumns: no visible global function definition for ‘setNames’
fillColumns: no visible global function definition for ‘setNames’
Undefined global functions or variables:
setNames
Consider adding
importFrom("stats", "setNames")
to your NAMESPACE file.
Version: 0.1.6
checking examples ... ERROR ``` ...
rename(xs, x0 = x1) $x0 [1] 1 2 3
$x2 [1] 2 3 4 5
$x3 $x3[[1]] [1] "alpha"
$x3[[2]] [1] "beta" "gamma"
select(xs, -x3) Error in select.list(xs, -x3) : select.list() cannot be used non-interactively Calls: select -> select.list Execution halted ```
checking re-building of vignette outputs ... WARNING ``` ... Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Attaching package: 'lplyr'
The following object is masked from 'package:dplyr':
pull
Quitting from lines 22-30 (lplyr-vignette.Rmd) Error: processing vignette 'lplyr-vignette.Rmd' failed with diagnostics: select.list() cannot be used non-interactively Execution halted ```
Version: 0.1.2
checking package dependencies ... ERROR ``` Package required but not available: ‘LPmerge’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```
Version: 0.6.1
Namespace in Imports field not imported from: ‘lazyeval’
All declared Imports should be used.
Version: 0.2.5
Packages unavailable to check Rd xrefs: ‘ggplot2’, ‘pander’, ‘pixiedust’
Version: 1.8.1
checking installed package size ... NOTE
installed size is 8.7Mb
sub-directories of 1Mb or more:
extdata 6.7Mb
checking R code for possible problems ... NOTE
.mgDb_annotateFeatures: no visible binding for global variable
‘db_keys’
.select.taxa: no visible binding for global variable ‘Keys’
.select.taxa: no visible binding for global variable ‘.’
aggregate_taxa: no visible binding for global variable ‘.’
aggregate_taxa: no visible binding for global variable ‘index’
vignette_pheno_data: no visible global function definition for
‘read.csv’
Undefined global functions or variables:
. Keys db_keys index read.csv
Consider adding
importFrom("utils", "read.csv")
to your NAMESPACE file.
Version: 0.1.1
Packages unavailable to check Rd xrefs: ‘lme4’, ‘rstanarm’
Version: 1.1.0
checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘manipulate’
checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘cubature’
Version: 0.3.0
Namespaces in Imports field not imported from:
‘MASS’ ‘caret’ ‘ggformula’ ‘knitr’ ‘testthat’ ‘tidyverse’
All declared Imports should be used.
Version: 0.8.9
Installation failed.
See ‘/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/checks/mrgsolve/new/mrgsolve.Rcheck/00install.out’ for details.
* installing *source* package ‘mrgsolve’ ...
** package ‘mrgsolve’ successfully unpacked and MD5 sums checked
** libs
ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/RcppArmadillo/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/BH/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c RcppExports.cpp -o RcppExports.o
ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/RcppArmadillo/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/BH/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c dataobject.cpp -o dataobject.o
ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/RcppArmadillo/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/BH/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c datarecord.cpp -o datarecord.o
ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/RcppArmadillo/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/BH/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c devtran.cpp -o devtran.o
ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/RcppArmadillo/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/BH/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c housemodel-mread-source.cpp -o housemodel-mread-source.o
ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/RcppArmadillo/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/BH/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c mrgsolve.cpp -o mrgsolve.o
ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/RcppArmadillo/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/BH/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c mrgsolve_init.cpp -o mrgsolve_init.o
ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/RcppArmadillo/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/BH/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c odepack_dlsoda.cpp -o odepack_dlsoda.o
ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/RcppArmadillo/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/BH/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c odeproblem.cpp -o odeproblem.o
gfortran -fPIC -g -O2 -c opk_dlsoda_mrg.f -o opk_dlsoda_mrg.o
gfortran -fPIC -g -O2 -c opkda1_mrg.f -o opkda1_mrg.o
gfortran -fPIC -g -O2 -c opkda2_mrg.f -o opkda2_mrg.o
ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/RcppArmadillo/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/BH/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c quick.cpp -o quick.o
ccache clang++ -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 mrgsolve.so RcppExports.o dataobject.o datarecord.o devtran.o housemodel-mread-source.o mrgsolve.o mrgsolve_init.o odepack_dlsoda.o odeproblem.o opk_dlsoda_mrg.o opkda1_mrg.o opkda2_mrg.o quick.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
ld: library not found for -lquadmath
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [mrgsolve.so] Error 1
ERROR: compilation failed for package ‘mrgsolve’
* removing ‘/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/checks/mrgsolve/new/mrgsolve.Rcheck/mrgsolve’
* installing *source* package ‘mrgsolve’ ...
** package ‘mrgsolve’ successfully unpacked and MD5 sums checked
** libs
ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/RcppArmadillo/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/BH/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c RcppExports.cpp -o RcppExports.o
ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/RcppArmadillo/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/BH/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c dataobject.cpp -o dataobject.o
ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/RcppArmadillo/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/BH/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c datarecord.cpp -o datarecord.o
ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/RcppArmadillo/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/BH/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c devtran.cpp -o devtran.o
ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/RcppArmadillo/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/BH/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c housemodel-mread-source.cpp -o housemodel-mread-source.o
ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/RcppArmadillo/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/BH/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c mrgsolve.cpp -o mrgsolve.o
ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/RcppArmadillo/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/BH/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c mrgsolve_init.cpp -o mrgsolve_init.o
ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/RcppArmadillo/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/BH/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c odepack_dlsoda.cpp -o odepack_dlsoda.o
ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/RcppArmadillo/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/BH/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c odeproblem.cpp -o odeproblem.o
gfortran -fPIC -g -O2 -c opk_dlsoda_mrg.f -o opk_dlsoda_mrg.o
gfortran -fPIC -g -O2 -c opkda1_mrg.f -o opkda1_mrg.o
gfortran -fPIC -g -O2 -c opkda2_mrg.f -o opkda2_mrg.o
ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/Rcpp/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/RcppArmadillo/include" -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/mrgsolve/BH/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c quick.cpp -o quick.o
ccache clang++ -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 mrgsolve.so RcppExports.o dataobject.o datarecord.o devtran.o housemodel-mread-source.o mrgsolve.o mrgsolve_init.o odepack_dlsoda.o odeproblem.o opk_dlsoda_mrg.o opkda1_mrg.o opkda2_mrg.o quick.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
ld: library not found for -lquadmath
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [mrgsolve.so] Error 1
ERROR: compilation failed for package ‘mrgsolve’
* removing ‘/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/checks/mrgsolve/old/mrgsolve.Rcheck/mrgsolve’
Version: 0.7.6
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Unable to find any JVMs matching version "(null)".
No Java runtime present, try --request to install.
Quitting from lines 197-201 (parameter-table.Rmd)
Error: processing vignette 'parameter-table.Rmd' failed with diagnostics:
package 'ReporteRsjars' could not be loaded
Execution halted
checking dependencies in R code ... NOTE
Unable to find any JVMs matching version "(null)".
No Java runtime present, try --request to install.
Version: 0.1.2
Packages unavailable to check Rd xrefs: ‘ensurer’, ‘validate’
Version: 2.1-5
Installation failed.
See ‘/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/checks/openair/new/openair.Rcheck/00install.out’ for details.
* installing *source* package ‘openair’ ...
** package ‘openair’ successfully unpacked and MD5 sums checked
** libs
ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/openair/Rcpp/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c cluster.cpp -o cluster.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/openair/Rcpp/include" -I/usr/local/include -fPIC -Wall -pedantic -O0 -c init.c -o init.o
ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/openair/Rcpp/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c rolling.cpp -o rolling.o
ccache clang++ -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 openair.so cluster.o init.o rolling.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
ld: library not found for -lquadmath
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [openair.so] Error 1
ERROR: compilation failed for package ‘openair’
* removing ‘/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/checks/openair/new/openair.Rcheck/openair’
* installing *source* package ‘openair’ ...
** package ‘openair’ successfully unpacked and MD5 sums checked
** libs
ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/openair/Rcpp/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c cluster.cpp -o cluster.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/openair/Rcpp/include" -I/usr/local/include -fPIC -Wall -pedantic -O0 -c init.c -o init.o
ccache clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/openair/Rcpp/include" -I/usr/local/include -fPIC -arch x86_64 -ftemplate-depth-256 -Wall -pedantic -O0 -c rolling.cpp -o rolling.o
ccache clang++ -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 openair.so cluster.o init.o rolling.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
ld: library not found for -lquadmath
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [openair.so] Error 1
ERROR: compilation failed for package ‘openair’
* removing ‘/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/checks/openair/old/openair.Rcheck/openair’
Version: 0.1.0
checking examples ... ERROR ``` Running examples in ‘parsemsf-Ex.R’ failed The error most likely occurred in:
Name: make_area_table
Title: Make a table of peptide areas
Aliases: make_area_table
** Examples
make_area_table(parsemsf_example("test_db.msf")) Error: The dbplyr package is required to communicate with database backends. Execution halted ```
checking tests ...
``
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
10: src_sqlite(msf_file)
11: check_dbplyr()
12: check_pkg("dbplyr", "communicate with database backends", install = FALSE)
13: glubort(NULL, "The {name} package is required to {reason}.", if (install) "\nPlease install it with
install.packages(\"{name}\")`")
14: .abort(text)
Error: The dbplyr package is required to communicate with database backends. testthat results ================================================================ OK: 0 SKIPPED: 0 FAILED: 3 1. Error: make_area_table creates a data frame with the correct column names (@test_make_area_table.R#16) 2. Error: make_pep_table creates a data frame with the correct column names (@test_make_pep_table.R#13) 3. Error: map_peptides creates a data frame with the correct column names (@test_map_peptides.R#16)
Error: testthat unit tests failed Execution halted ```
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
Quitting from lines 20-25 (introduction.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
The dbplyr package is required to communicate with database backends.
Execution halted
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘RSQLite’
All declared Imports should be used.
Version: 2.0.0
Namespace in Imports field not imported from: ‘purrr’
All declared Imports should be used.
Version: 0.0.2
Namespace in Imports field not imported from: ‘lazyeval’
All declared Imports should be used.
Version: 0.1.0
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: testthat results ================================================================ OK: 139 SKIPPED: 0 FAILED: 10
Error: testthat unit tests failed Execution halted ```
Version: 0.5.0
checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘shiny’
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘ggplot2’
All declared Imports should be used.
Version: 2.1.2
Note: found 44 marked UTF-8 strings
Version: 1.0.1
checking examples ... ERROR ``` Running examples in ‘rgho-Ex.R’ failed The error most likely occurred in:
Name: get_gho_data
Title: Returns GHO Data
Aliases: get_gho_data
** Examples
result <- get_gho_data( + dimension = "GHO", + code = "MDG_0000000001" + ) Error: parse error: premature EOF { "copyright": "(c) World Healt (right here) ------^ Execution halted ```
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
Quitting from lines 36-38 (a-intro.Rmd)
Error: processing vignette 'a-intro.Rmd' failed with diagnostics:
parse error: premature EOF
{ "copyright": "(c) World Healt
(right here) ------^
Execution halted
Version: 2.0.7
Packages suggested but not available for checking: ‘rrdf’ ‘Sxslt’
Version: 0.2.2
Version: 1.2
GNU make is a SystemRequirements.
Version: 0.4.0
Error in re-building vignettes:
...
Quitting from lines 22-29 (introduction.Rmd)
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
Missing API key; ?sc_key for details
Execution halted
Version: 1.3
Namespace in Imports field not imported from: ‘R6’
All declared Imports should be used.
Version: 0.5-4
Installation failed.
See ‘/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/checks/sf/new/sf.Rcheck/00install.out’ for details.
* installing *source* package ‘sf’ ...
** package ‘sf’ successfully unpacked and MD5 sums checked
configure: CC: clang
configure: CXX: ccache clang++
checking for gdal-config... no
no
configure: error: gdal-config not found or not executable.
ERROR: configuration failed for package ‘sf’
* removing ‘/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/checks/sf/new/sf.Rcheck/sf’
* installing *source* package ‘sf’ ...
** package ‘sf’ successfully unpacked and MD5 sums checked
configure: CC: clang
configure: CXX: ccache clang++
checking for gdal-config... no
no
configure: error: gdal-config not found or not executable.
ERROR: configuration failed for package ‘sf’
* removing ‘/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/checks/sf/old/sf.Rcheck/sf’
Version: 0.1.8
Note: found 2 marked UTF-8 strings
Version: 0.1.0
checking tests ... ``` ERROR Running the tests in ‘tests/test-all.R’ failed. Last 13 lines of output: 100 43558 100 43558 0 0 457k 0 --:--:-- --:--:-- --:--:-- 457k
testthat results ================================================================ OK: 304 SKIPPED: 2 FAILED: 1 1. Error: spelling errors (@test-spelling.R#19)
Error: testthat unit tests failed In addition: Warning message: In fun(libname, pkgname) : couldn't connect to display "" Execution halted ```
checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘CircStats’ ‘RandomFields’ ‘grDevices’ ‘sp’
All declared Imports should be used.
Version: 0.6.3
Version: 0.3.0
checking tests ...
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(statisticalModeling)
Loading required package: ggplot2
>
> test_check("statisticalModeling")
Error: gwm() has been removed from `mosaic'.
It will be replaced by better tools in `mosaicModel'.
testthat results ================================================================
OK: 21 SKIPPED: 0 FAILED: 0
Execution halted
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
Quitting from lines 303-306 (modeling.Rmd)
Error: processing vignette 'modeling.Rmd' failed with diagnostics:
Invalid formula type for gf_point.
Execution halted
checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘magrittr’ ‘rpart’
All declared Imports should be used.
Version: 0.2.0
Namespaces in Imports field not imported from:
‘devtools’ ‘lazyeval’ ‘lubridate’ ‘tidyr’
All declared Imports should be used.
Version: 0.13.0
checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘rmdformats’
checking data for non-ASCII characters ... NOTE
Note: found 3 marked UTF-8 strings
Version: 0.1.0
Namespaces in Imports field not imported from:
‘knitr’ ‘lazyeval’ ‘rlang’
All declared Imports should be used.
Version: 0.1.2
Namespace in Imports field not imported from: ‘PerformanceAnalytics’
All declared Imports should be used.
Version: 0.5.3
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output:
testthat results ================================================================ OK: 191 SKIPPED: 0 FAILED: 9 1. Failure: Test all stock.index options to ensure no issues during fetch. (@test_tq_index.R#22) 2. Failure: Test all stock.index options to ensure no issues during fetch. (@test_tq_index.R#22) 3. Failure: Test all stock.index options to ensure no issues during fetch. (@test_tq_index.R#22) 4. Failure: Test all stock.index options to ensure no issues during fetch. (@test_tq_index.R#22) 5. Failure: Test all stock.index options to ensure no issues during fetch. (@test_tq_index.R#22) 6. Failure: Test all stock.index options to ensure no issues during fetch. (@test_tq_index.R#22) 7. Failure: Test all stock.index options to ensure no issues during fetch. (@test_tq_index.R#22) 8. Failure: Test all stock.index options to ensure no issues during fetch. (@test_tq_index.R#22) 9. Failure: Test all stock.index options to ensure no issues during fetch. (@test_tq_index.R#22)
Error: testthat unit tests failed Execution halted ```
checking re-building of vignette outputs ... WARNING ``` ... Reason: image not found
Getting data...
Getting holdings for DOW Unable to find any JVMs matching version "(null)". No Java runtime present, try --request to install. Warning: running command '/usr/libexec/java_home' had status 1 Warning in tq_index("DOW") : Error at DOW during download. Error: .onLoad failed in loadNamespace() for 'rJava', details: call: dyn.load(file, DLLpath = DLLpath, ...) error: unable to load shared object '/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/tidyquant/rJava/libs/rJava.so': dlopen(/Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/tidyquant/rJava/libs/rJava.so, 6): Library not loaded: @rpath/libjvm.dylib Referenced from: /Users/lionel/Dropbox/Projects/R/hadley/lazyeval/revdep/library/tidyquant/rJava/libs/rJava.so Reason: image not found
Quitting from lines 105-108 (TQ03-scaling-and-modeling-with-tidyquant.Rmd) Error: processing vignette 'TQ03-scaling-and-modeling-with-tidyquant.Rmd' failed with diagnostics: subscript out of bounds Execution halted ```
checking dependencies in R code ... NOTE
Unable to find any JVMs matching version "(null)".
No Java runtime present, try --request to install.
Namespaces in Imports field not imported from:
‘broom’ ‘curl’ ‘devtools’ ‘rvest’ ‘timeSeries’ ‘tseries’ ‘zoo’
All declared Imports should be used.
Version: 0.1.0
Namespaces in Imports field not imported from:
‘devtools’ ‘forecast’
All declared Imports should be used.
Version: 0.1.2
Namespace in Imports field not imported from: ‘purrr’
All declared Imports should be used.
Version: 1.2.0
Namespaces in Imports field not imported from:
‘iterators’ ‘knitr’ ‘testthat’
All declared Imports should be used.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.