Version: 0.0.1
Namespaces in Imports field not imported from:
‘DBI’ ‘assertthat’ ‘tibble’
All declared Imports should be used.
Version: 0.15.0
installed size is 6.0Mb
sub-directories of 1Mb or more:
R 2.1Mb
doc 2.0Mb
htmlwidgets 1.1Mb
Version: 0.7
aw_map: no visible global function definition for ‘browseURL’
(/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/AntWeb/new/AntWeb.Rcheck/00_pkg_src/AntWeb/R/aw_map.R:52)
Undefined global functions or variables:
browseURL
Consider adding
importFrom("utils", "browseURL")
to your NAMESPACE file.
Version: 0.3.2
Note: found 552 marked UTF-8 strings
Version: 0.2.0
Installation failed.
See ‘/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/awsjavasdk/new/awsjavasdk.Rcheck/00install.out’ for details.
* installing *source* package ‘awsjavasdk’ ...
** package ‘awsjavasdk’ successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
Error : .onLoad failed in loadNamespace() for 'rJava', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/Users/hadley/Documents/devtools/assertthat/revdep/library.noindex/awsjavasdk/rJava/libs/rJava.so':
dlopen(/Users/hadley/Documents/devtools/assertthat/revdep/library.noindex/awsjavasdk/rJava/libs/rJava.so, 6): Library not loaded: /Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home/lib/server/libjvm.dylib
Referenced from: /Users/hadley/Documents/devtools/assertthat/revdep/library.noindex/awsjavasdk/rJava/libs/rJava.so
Reason: image not found
ERROR: lazy loading failed for package ‘awsjavasdk’
* removing ‘/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/awsjavasdk/new/awsjavasdk.Rcheck/awsjavasdk’
* installing *source* package ‘awsjavasdk’ ...
** package ‘awsjavasdk’ successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
Error : .onLoad failed in loadNamespace() for 'rJava', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/Users/hadley/Documents/devtools/assertthat/revdep/library.noindex/awsjavasdk/rJava/libs/rJava.so':
dlopen(/Users/hadley/Documents/devtools/assertthat/revdep/library.noindex/awsjavasdk/rJava/libs/rJava.so, 6): Library not loaded: /Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home/lib/server/libjvm.dylib
Referenced from: /Users/hadley/Documents/devtools/assertthat/revdep/library.noindex/awsjavasdk/rJava/libs/rJava.so
Reason: image not found
ERROR: lazy loading failed for package ‘awsjavasdk’
* removing ‘/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/awsjavasdk/old/awsjavasdk.Rcheck/awsjavasdk’
Version: 0.4.0
checking package dependencies ... ERROR ``` Packages required but not available: ‘googleAuthR’ ‘googleCloudStorageR’
Packages suggested but not available for checking: ‘shiny’ ‘data.table’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```
Version: 0.1.1
checking package dependencies ... ERROR ``` Package required but not available: ‘semver’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```
Version: 1.0.0
checking package dependencies ... ERROR ``` Package required but not available: ‘reutils’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```
Version: 1.8.1
Installation failed.
See ‘/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/BPRMeth/new/BPRMeth.Rcheck/00install.out’ for details.
* installing *source* package ‘BPRMeth’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/hadley/Documents/devtools/assertthat/revdep/library.noindex/BPRMeth/Rcpp/include" -I"/Users/hadley/Documents/devtools/assertthat/revdep/library.noindex/BPRMeth/RcppArmadillo/include" -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang: error: unsupported option '-fopenmp'
make: *** [RcppExports.o] Error 1
ERROR: compilation failed for package ‘BPRMeth’
* removing ‘/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/BPRMeth/new/BPRMeth.Rcheck/BPRMeth’
* installing *source* package ‘BPRMeth’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/hadley/Documents/devtools/assertthat/revdep/library.noindex/BPRMeth/Rcpp/include" -I"/Users/hadley/Documents/devtools/assertthat/revdep/library.noindex/BPRMeth/RcppArmadillo/include" -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang: error: unsupported option '-fopenmp'
make: *** [RcppExports.o] Error 1
ERROR: compilation failed for package ‘BPRMeth’
* removing ‘/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/BPRMeth/old/BPRMeth.Rcheck/BPRMeth’
Version: 0.4.6
Package unavailable to check Rd xrefs: ‘breathteststan’
Version: 1.0.0
checking package dependencies ... ERROR ``` Package required but not available: ‘Rdpack’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```
Version: 1.2.0
checking package dependencies ... ERROR ``` Packages required but not available: ‘Matrix.utils’ ‘grr’ ‘GenomicFeatures’ ‘InteractionSet’ ‘GenomicInteractions’
Packages suggested but not available for checking: ‘org.Mm.eg.db’ ‘TxDb.Mmusculus.UCSC.mm9.knownGene’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```
Version: 1.2.3
ConstructModel: warning in AddDynamicRegression(ss, formula, data =
data, sigma.mean.prior = sigma.mean.prior): partial argument match of
'sigma.mean.prior' to 'sigma.mean.prior.DEPRECATED'
(/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/CausalImpact/new/CausalImpact.Rcheck/00_pkg_src/CausalImpact/R/impact_model.R:232-233)
Version: 1.0.15
aggregate_nearby_peaks: no visible binding for global variable 'val'
(/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/cicero/new/cicero.Rcheck/00_pkg_src/cicero/R/aggregate.R:37)
assemble_connections: no visible binding for global variable 'value'
(/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/cicero/new/cicero.Rcheck/00_pkg_src/cicero/R/runCicero.R:640-641)
find_overlapping_ccans: no visible binding for global variable 'CCAN'
(/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/cicero/new/cicero.Rcheck/00_pkg_src/cicero/R/runCicero.R:919-922)
generate_windows: no visible binding for global variable 'V1'
(/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/cicero/new/cicero.Rcheck/00_pkg_src/cicero/R/runCicero.R:663-667)
plot_accessibility_in_pseudotime: no visible binding for global
variable 'f_id'
(/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/cicero/new/cicero.Rcheck/00_pkg_src/cicero/R/plotting.R:676-695)
Undefined global functions or variables:
CCAN V1 f_id val value
Version: 0.2.1
Installation failed.
See ‘/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/circumplex/new/circumplex.Rcheck/00install.out’ for details.
* installing *source* package ‘circumplex’ ...
** package ‘circumplex’ successfully unpacked and MD5 sums checked
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/hadley/Documents/devtools/assertthat/revdep/library.noindex/circumplex/Rcpp/include" -I"/Users/hadley/Documents/devtools/assertthat/revdep/library.noindex/circumplex/RcppArmadillo/include" -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang: error: unsupported option '-fopenmp'
make: *** [RcppExports.o] Error 1
ERROR: compilation failed for package ‘circumplex’
* removing ‘/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/circumplex/new/circumplex.Rcheck/circumplex’
* installing *source* package ‘circumplex’ ...
** package ‘circumplex’ successfully unpacked and MD5 sums checked
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/hadley/Documents/devtools/assertthat/revdep/library.noindex/circumplex/Rcpp/include" -I"/Users/hadley/Documents/devtools/assertthat/revdep/library.noindex/circumplex/RcppArmadillo/include" -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang: error: unsupported option '-fopenmp'
make: *** [RcppExports.o] Error 1
ERROR: compilation failed for package ‘circumplex’
* removing ‘/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/circumplex/old/circumplex.Rcheck/circumplex’
Version: 0.3.0
Namespace in Imports field not imported from: ‘bibtex’
All declared Imports should be used.
Version: 0.1.0
Namespace in Imports field not imported from: ‘tea’
All declared Imports should be used.
Version: 1.12.0
Installation failed.
See ‘/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/DChIPRep/new/DChIPRep.Rcheck/00install.out’ for details.
* installing *source* package ‘DChIPRep’ ...
** R
** data
*** moving datasets to lazyload DB
Warning: namespace ‘DChIPRep’ is not available and has been replaced
by .GlobalEnv when processing object ‘testData’
Warning: namespace ‘DChIPRep’ is not available and has been replaced
by .GlobalEnv when processing object ‘testData’
** exec
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
there is no package called ‘GO.db’
ERROR: lazy loading failed for package ‘DChIPRep’
* removing ‘/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/DChIPRep/new/DChIPRep.Rcheck/DChIPRep’
* installing *source* package ‘DChIPRep’ ...
** R
** data
*** moving datasets to lazyload DB
Warning: namespace ‘DChIPRep’ is not available and has been replaced
by .GlobalEnv when processing object ‘testData’
Warning: namespace ‘DChIPRep’ is not available and has been replaced
by .GlobalEnv when processing object ‘testData’
** exec
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
there is no package called ‘GO.db’
ERROR: lazy loading failed for package ‘DChIPRep’
* removing ‘/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/DChIPRep/old/DChIPRep.Rcheck/DChIPRep’
Version: 1.4.1
installed size is 6.0Mb
sub-directories of 1Mb or more:
R 1.2Mb
data 1.4Mb
doc 3.1Mb
Version: 0.6.0
GNU make is a SystemRequirements.
Version: 0.2.0
Namespaces in Imports field not imported from:
‘dplyr’ ‘proxy’
All declared Imports should be used.
Version: 0.8.0.1
checking installed package size ... NOTE
installed size is 6.8Mb
sub-directories of 1Mb or more:
R 2.1Mb
libs 3.0Mb
checking data for non-ASCII characters ... NOTE
Note: found 4 marked UTF-8 strings
Version: 1.11.0
Namespace in Imports field not imported from: ‘magrittr’
All declared Imports should be used.
Version: 0.4.4
checking installed package size ... NOTE
installed size is 7.7Mb
sub-directories of 1Mb or more:
libs 7.2Mb
checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘methods’ ‘rstantools’
All declared Imports should be used.
checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
Version: 1.0.0
installed size is 11.2Mb
sub-directories of 1Mb or more:
data 3.0Mb
doc 1.0Mb
extdata 6.5Mb
Version: 1.2
Namespaces in Imports field not imported from:
‘DT’ ‘shinydashboard’
All declared Imports should be used.
Version: 0.1.2
GNU make is a SystemRequirements.
Version: 0.7.0
Namespace in Imports field not imported from: ‘R6’
All declared Imports should be used.
Version: 1.7.0.0
Packages suggested but not available for checking:
‘taxstats’ ‘taxstats1516’
Version: 0.15.2
checking installed package size ... NOTE
installed size is 5.3Mb
sub-directories of 1Mb or more:
doc 4.6Mb
checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘d3heatmap’
Version: 0.7.0
installed size is 9.2Mb
sub-directories of 1Mb or more:
doc 3.7Mb
htmlwidgets 4.0Mb
Version: 1.2.1
checking re-building of vignette outputs ... WARNING ``` ... Attaching package: 'dendextend'
The following object is masked from 'package:stats':
cutree
======================================== circlize version 0.4.5 CRAN page: https://cran.r-project.org/package=circlize Github page: https://github.com/jokergoo/circlize Documentation: http://jokergoo.github.io/circlize_book/book/
If you use it in published research, please cite: Gu, Z. circlize implements and enhances circular visualization in R. Bioinformatics 2014. ========================================
Quitting from lines 58-71 (HMP16SData.Rmd) Error: processing vignette 'HMP16SData.Rmd' failed with diagnostics: there is no package called 'curatedMetagenomicData' Execution halted ```
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘curatedMetagenomicData’
checking installed package size ... NOTE
installed size is 19.1Mb
sub-directories of 1Mb or more:
doc 1.5Mb
extdata 17.4Mb
Version: 4.4.0
checking tests ...
``
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
Fontconfig error: "/Users/hadley/Documents/devtools/assertthat/revdep/library.noindex/huxtable/magick/etc/fonts/conf.d/90-synthetic.conf", line 6: invalid attribute 'version'
Fontconfig error: Cannot load default config file
[31m──[39m [31m1. Failure: huxreg copes with different models (@test-huxreg.R#31) [39m [31m───────────[39m
hr <- huxreg(lm1, lm2, glm1)` produced warnings.
[31m──[39m [31m2. Failure: Data written in appropriate format (@test-openxlsx.R#101) [39m [31m────────[39m
openxlsx::saveWorkbook(wb, file = "test-xlsx.xlsx", overwrite = TRUE)
produced messages.
══ testthat results ═════════════════════════════════════════════════════════════ OK: 888 SKIPPED: 57 FAILED: 2 1. Failure: huxreg copes with different models (@test-huxreg.R#31) 2. Failure: Data written in appropriate format (@test-openxlsx.R#101)
Error: testthat unit tests failed Execution halted ```
checking installed package size ... NOTE
installed size is 5.3Mb
sub-directories of 1Mb or more:
R 2.1Mb
doc 2.9Mb
Version: 1.0.0
Namespaces in Imports field not imported from:
‘EQL’ ‘knitr’ ‘rmarkdown’
All declared Imports should be used.
Version: 0.6.0
installed size is 6.1Mb
sub-directories of 1Mb or more:
libs 5.4Mb
Version: 2.0.0
Namespaces in Imports field not imported from:
‘MASS’ ‘stats’
All declared Imports should be used.
Version: 0.5.0
Namespaces in Imports field not imported from:
‘ProjectTemplate’ ‘devtools’ ‘plyr’ ‘survival’
All declared Imports should be used.
Version: 1.1-2
Package unavailable to check Rd xrefs: ‘Familias’
Version: 1.2.1
installed size is 5.9Mb
sub-directories of 1Mb or more:
data 3.8Mb
Version: 1.2.1
checking installed package size ... NOTE
installed size is 14.9Mb
sub-directories of 1Mb or more:
doc 2.6Mb
www 11.5Mb
checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
'GEOquery:::getDirListing' 'opencpu:::rookhandler'
'opencpu:::tmp_root' 'opencpu:::win_or_mac'
See the note in ?`:::` about the use of this operator.
Version: 18.4.17
checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘odbc’
checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘colorspace’ ‘lubridate’
All declared Imports should be used.
Version: 1.0.3
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 1: read_packages_file(pf[1], mirror = "m1", repodir = "r1", platform = "source", rversion = "*") at testthat/test-packages-gz.R:88 2: as_tibble(read.dcf.gz(path)) at /Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/pkgcache/new/pkgcache.Rcheck/00_pkg_src/pkgcache/R/packages-gz.R:19 3: read.dcf.gz(path) at /Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/pkgcache/new/pkgcache.Rcheck/00_pkg_src/pkgcache/R/packages-gz.R:19 4: gzfile(x, open = "r") at /Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/pkgcache/new/pkgcache.Rcheck/00_pkg_src/pkgcache/R/utils.R:32
══ testthat results ═════════════════════════════════════════════════════════════ OK: 282 SKIPPED: 25 FAILED: 5 1. Error: load_primary_pkgs (@test-metadata-cache.R#177) 2. Error: update_replica_rds (@test-metadata-cache.R#236) 3. Error: read_packages_file (@test-packages-gz.R#63) 4. Error: packages_parse_deps (@test-packages-gz.R#71) 5. Error: merge_packages_data (@test-packages-gz.R#88)
Error: testthat unit tests failed Execution halted ```
Version: 4.0.2
Packages suggested but not available for checking: ‘gurobi’ ‘Rsymphony’
Version: 1.0.3
checking re-building of vignette outputs ... WARNING ``` ...
Loading required package: ProtGenerics
This is MSnbase version 2.8.3 Visit https://lgatto.github.io/MSnbase/ to get started.
Attaching package: 'MSnbase'
The following object is masked from 'package:stats':
smooth
The following object is masked from 'package:base':
trimws
Quitting from lines 67-71 (qPLEXanalyzer.rnw) Error: processing vignette 'qPLEXanalyzer.rnw' failed with diagnostics: there is no package called 'gridExtra' Execution halted ```
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘qPLEXdata’
checking R code for possible problems ... NOTE
...
rliPlot: no visible binding for global variable ‘logInt’
(/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/qPLEXanalyzer/new/qPLEXanalyzer.Rcheck/00_pkg_src/qPLEXanalyzer/R/plots.R:599-621)
rliPlot: no visible binding for global variable ‘medianLogInt’
(/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/qPLEXanalyzer/new/qPLEXanalyzer.Rcheck/00_pkg_src/qPLEXanalyzer/R/plots.R:599-621)
summarizeIntensities: no visible binding for global variable
‘Accessions’
(/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/qPLEXanalyzer/new/qPLEXanalyzer.Rcheck/00_pkg_src/qPLEXanalyzer/R/Allfunctions.R:55-60)
summarizeIntensities: no visible binding for global variable
‘Sequences’
(/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/qPLEXanalyzer/new/qPLEXanalyzer.Rcheck/00_pkg_src/qPLEXanalyzer/R/Allfunctions.R:55-60)
summarizeIntensities: no visible binding for global variable
‘Accessions’
(/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/qPLEXanalyzer/new/qPLEXanalyzer.Rcheck/00_pkg_src/qPLEXanalyzer/R/Allfunctions.R:62-68)
summarizeIntensities: no visible binding for global variable ‘Count’
(/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/qPLEXanalyzer/new/qPLEXanalyzer.Rcheck/00_pkg_src/qPLEXanalyzer/R/Allfunctions.R:62-68)
Undefined global functions or variables:
. Accessions AveExpr B Cor CorTxt Count GeneSymbol Grouping_column
Intensity Mean Modifications PeptideID RawIntensity RowID SampleName
Sequence Sequences Variance X Y adj.P.Val controlLogFoldChange group
logFC logInt logIntensity meanscaledIntensity medianLogInt
normalizedIntensities scaledIntensity scalingFactors x xend y yend
checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘gridExtra’
Version: 0.4.3
GNU make is a SystemRequirements.
Version: 0.1.1
Namespace in Imports field not imported from: ‘dplyr’
All declared Imports should be used.
Version: 0.1.3
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘gurobi’
checking installed package size ... NOTE
installed size is 6.7Mb
sub-directories of 1Mb or more:
data 3.6Mb
doc 1.4Mb
Version: 1.3-7
checking installed package size ... NOTE
installed size is 5.6Mb
sub-directories of 1Mb or more:
R 1.1Mb
doc 1.9Mb
libs 2.2Mb
checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
Version: 0.4.1
Note: found 31 marked UTF-8 strings
Version: 0.3.0
Namespaces in Imports field not imported from:
‘httpuv’ ‘utils’
All declared Imports should be used.
Version: 0.1.0
but_last: no visible global function definition for ‘head’
first: no visible global function definition for ‘head’
last: no visible global function definition for ‘tail’
preview_frames: no visible global function definition for ‘str’
(/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/rprime/new/rprime.Rcheck/00_pkg_src/rprime/R/preview.R:37)
print.EprimeFrame: no visible global function definition for ‘str’
print.FrameList: no visible global function definition for ‘str’
Undefined global functions or variables:
head str tail
Consider adding
importFrom("utils", "head", "str", "tail")
to your NAMESPACE file.
Version: 0.2.1
Installation failed.
See ‘/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/rrd/new/rrd.Rcheck/00install.out’ for details.
* installing *source* package ‘rrd’ ...
** package ‘rrd’ successfully unpacked and MD5 sums checked
** libs
ccache clang -Qunused-arguments -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c registerDynamicSymbol.c -o registerDynamicSymbol.o
ccache clang -Qunused-arguments -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c rrd.c -o rrd.o
rrd.c:1:10: fatal error: 'rrd.h' file not found
#include <rrd.h>
^~~~~~~
1 error generated.
make: *** [rrd.o] Error 1
ERROR: compilation failed for package ‘rrd’
* removing ‘/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/rrd/new/rrd.Rcheck/rrd’
* installing *source* package ‘rrd’ ...
** package ‘rrd’ successfully unpacked and MD5 sums checked
** libs
ccache clang -Qunused-arguments -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c registerDynamicSymbol.c -o registerDynamicSymbol.o
ccache clang -Qunused-arguments -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c rrd.c -o rrd.o
rrd.c:1:10: fatal error: 'rrd.h' file not found
#include <rrd.h>
^~~~~~~
1 error generated.
make: *** [rrd.o] Error 1
ERROR: compilation failed for package ‘rrd’
* removing ‘/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/rrd/old/rrd.Rcheck/rrd’
Version: 1.12.1
checking examples ... ERROR ``` Running examples in ‘RTCGA-Ex.R’ failed The error most likely occurred in:
Name: boxplotTCGA
Title: Create Boxplots for TCGA Datasets
Aliases: boxplotTCGA
** Examples
library(RTCGA.rnaseq) Error in library(RTCGA.rnaseq) : there is no package called ‘RTCGA.rnaseq’ Execution halted ```
checking tests ...
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(RTCGA)
Welcome to the RTCGA (version: 1.12.1).
> library(RTCGA.rnaseq)
Error in library(RTCGA.rnaseq) :
there is no package called 'RTCGA.rnaseq'
Execution halted
checking package dependencies ... NOTE
Packages suggested but not available for checking:
‘RTCGA.rnaseq’ ‘RTCGA.clinical’ ‘RTCGA.mutations’ ‘RTCGA.RPPA’
‘RTCGA.mRNA’ ‘RTCGA.miRNASeq’ ‘RTCGA.methylation’ ‘RTCGA.CNV’
‘RTCGA.PANCAN12’
checking R code for possible problems ... NOTE
...
(/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/RTCGA/new/RTCGA.Rcheck/00_pkg_src/RTCGA/R/ggbiplot.R:157-161)
ggbiplot: no visible binding for global variable ‘xvar’
(/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/RTCGA/new/RTCGA.Rcheck/00_pkg_src/RTCGA/R/ggbiplot.R:157-161)
ggbiplot: no visible binding for global variable ‘yvar’
(/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/RTCGA/new/RTCGA.Rcheck/00_pkg_src/RTCGA/R/ggbiplot.R:157-161)
ggbiplot: no visible binding for global variable ‘angle’
(/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/RTCGA/new/RTCGA.Rcheck/00_pkg_src/RTCGA/R/ggbiplot.R:157-161)
ggbiplot: no visible binding for global variable ‘hjust’
(/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/RTCGA/new/RTCGA.Rcheck/00_pkg_src/RTCGA/R/ggbiplot.R:157-161)
read.mutations: no visible binding for global variable ‘.’
(/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/RTCGA/new/RTCGA.Rcheck/00_pkg_src/RTCGA/R/readTCGA.R:383)
read.mutations: no visible binding for global variable ‘.’
(/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/RTCGA/new/RTCGA.Rcheck/00_pkg_src/RTCGA/R/readTCGA.R:386)
read.rnaseq: no visible binding for global variable ‘.’
(/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/RTCGA/new/RTCGA.Rcheck/00_pkg_src/RTCGA/R/readTCGA.R:372-375)
survivalTCGA: no visible binding for global variable ‘times’
(/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/RTCGA/new/RTCGA.Rcheck/00_pkg_src/RTCGA/R/survivalTCGA.R:101-137)
whichDateToUse: no visible binding for global variable ‘.’
(/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/RTCGA/new/RTCGA.Rcheck/00_pkg_src/RTCGA/R/downloadTCGA.R:167-168)
Undefined global functions or variables:
. angle hjust muted times varname xvar yvar
checking Rd cross-references ... NOTE
Packages unavailable to check Rd xrefs: ‘RTCGA.rnaseq’, ‘RTCGA.clinical’, ‘RTCGA.mutations’, ‘RTCGA.CNV’, ‘RTCGA.RPPA’, ‘RTCGA.mRNA’, ‘RTCGA.miRNASeq’, ‘RTCGA.methylation’
Version: 0.3.0.1.1
installed size is 8.1Mb
sub-directories of 1Mb or more:
include 2.5Mb
libs 4.9Mb
Version: 1.0.1
Namespaces in Imports field not imported from:
‘gtools’ ‘hashmap’ ‘reshape2’
All declared Imports should be used.
Version: 1.0.0
installed size is 6.8Mb
sub-directories of 1Mb or more:
R 4.1Mb
java 1.5Mb
Version: 0.1-0
Package unavailable to check Rd xrefs: ‘XML’
Version: 0.1.0
Namespaces in Imports field not imported from:
‘stringi’ ‘utils’
All declared Imports should be used.
Version: 0.1.4
Package unavailable to check Rd xrefs: ‘tm’
Version: 0.3.8
checking installed package size ... NOTE
installed size is 5.3Mb
sub-directories of 1Mb or more:
extdata 4.4Mb
checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘here’ ‘htmltools’ ‘scales’ ‘stringr’
All declared Imports should be used.
checking data for non-ASCII characters ... NOTE
Note: found 41 marked UTF-8 strings
Version: 1.2.0
checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘dplyr’
All declared Imports should be used.
checking data for non-ASCII characters ... NOTE
Note: found 88 marked UTF-8 strings
Version: 0.2.7
checking installed package size ... NOTE
installed size is 5.2Mb
sub-directories of 1Mb or more:
extdata 4.4Mb
checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘here’ ‘htmltools’ ‘scales’ ‘stringr’
All declared Imports should be used.
checking data for non-ASCII characters ... NOTE
Note: found 41 marked UTF-8 strings
Version: 1.0.1
Installation failed.
See ‘/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/updog/new/updog.Rcheck/00install.out’ for details.
* installing *source* package ‘updog’ ...
** package ‘updog’ successfully unpacked and MD5 sums checked
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/hadley/Documents/devtools/assertthat/revdep/library.noindex/updog/Rcpp/include" -I"/Users/hadley/Documents/devtools/assertthat/revdep/library.noindex/updog/RcppArmadillo/include" -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang: error: unsupported option '-fopenmp'
make: *** [RcppExports.o] Error 1
ERROR: compilation failed for package ‘updog’
* removing ‘/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/updog/new/updog.Rcheck/updog’
* installing *source* package ‘updog’ ...
** package ‘updog’ successfully unpacked and MD5 sums checked
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/hadley/Documents/devtools/assertthat/revdep/library.noindex/updog/Rcpp/include" -I"/Users/hadley/Documents/devtools/assertthat/revdep/library.noindex/updog/RcppArmadillo/include" -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang: error: unsupported option '-fopenmp'
make: *** [RcppExports.o] Error 1
ERROR: compilation failed for package ‘updog’
* removing ‘/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/updog/old/updog.Rcheck/updog’
Version: 1.6.1
checking examples ... ERROR ``` ... Loading required package: TxDb.Hsapiens.UCSC.hg38.knownGene Loading required package: GenomicFeatures Loading required package: AnnotationDbi Loading required package: Biobase Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: ‘AnnotationDbi’
The following object is masked from ‘package:dplyr’:
select
orgdb = org.Hs.eg.db Error: object 'org.Hs.eg.db' not found Execution halted ```
checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'getGenotypePalette':
getGenotypePalette
Code: function(old = FALSE)
Docs: function()
Argument names in code not in docs:
old
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
Quitting from lines 18-28 (wiggleplotr.Rmd)
Error: processing vignette 'wiggleplotr.Rmd' failed with diagnostics:
there is no package called 'EnsDb.Hsapiens.v86'
Execution halted
checking package dependencies ... NOTE
Packages suggested but not available for checking:
‘EnsDb.Hsapiens.v86’ ‘org.Hs.eg.db’
checking R code for possible problems ... NOTE
plotCoverage: no visible global function definition for ‘is’
(/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/wiggleplotr/new/wiggleplotr.Rcheck/00_pkg_src/wiggleplotr/R/wiggleplotr.R:184)
plotCoverage: no visible global function definition for ‘is’
(/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/wiggleplotr/new/wiggleplotr.Rcheck/00_pkg_src/wiggleplotr/R/wiggleplotr.R:185)
plotTranscripts: no visible global function definition for ‘is’
(/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/wiggleplotr/new/wiggleplotr.Rcheck/00_pkg_src/wiggleplotr/R/wiggleplotr.R:33)
plotTranscripts: no visible global function definition for ‘is’
(/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/wiggleplotr/new/wiggleplotr.Rcheck/00_pkg_src/wiggleplotr/R/wiggleplotr.R:34)
Undefined global functions or variables:
is
Consider adding
importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Version: 0.3.0
Namespace in Imports field not imported from: ‘dbplyr’
All declared Imports should be used.
Version: 0.1.0
Namespace in Imports field not imported from: ‘tibble’
All declared Imports should be used.
Version: 0.1.0
Namespaces in Imports field not imported from:
‘dplyr’ ‘ggplot2’ ‘lubridate’
All declared Imports should be used.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.