|setting |value | |:--------|:----------------------------| |version |R version 3.3.0 (2016-05-03) | |system |x86_64, darwin13.4.0 | |ui |X11 | |language |(EN) | |collate |en_US.UTF-8 | |tz |America/Chicago | |date |2016-06-23 |
|package | |version |date |source | |:--------------|:--|:----------|:----------|:--------------------------------| |assertthat | |0.1 |2013-12-06 |CRAN (R 3.3.0) | |BH | |1.60.0-2 |2016-05-07 |CRAN (R 3.3.0) | |covr | |2.1.0 |2016-06-21 |cran (@2.1.0) | |DBI | |0.4-1 |2016-05-08 |CRAN (R 3.3.0) | |dplyr | |0.4.3.9001 |2016-06-23 |local (hadley/dplyr@NA) | |dtplyr | |0.0.0.9001 |2016-06-23 |Github (hadley/dtplyr@57bd16f) | |ggplot2 | |2.1.0 |2016-03-01 |CRAN (R 3.3.0) | |knitr | |1.13 |2016-05-09 |CRAN (R 3.3.0) | |Lahman | |4.0-1 |2015-09-15 |CRAN (R 3.3.0) | |lazyeval | |0.2.0.9000 |2016-06-17 |Github (hadley/lazyeval@c155c3d) | |magrittr | |1.5 |2014-11-22 |CRAN (R 3.3.0) | |microbenchmark | |1.4-2.1 |2015-11-25 |CRAN (R 3.3.0) | |nycflights13 | |0.2.0 |2016-04-30 |CRAN (R 3.3.0) | |R6 | |2.1.2 |2016-01-26 |CRAN (R 3.3.0) | |Rcpp | |0.12.5 |2016-05-14 |CRAN (R 3.3.0) | |rmarkdown | |0.9.6 |2016-05-01 |CRAN (R 3.3.0) | |RMySQL | |0.10.9 |2016-05-08 |CRAN (R 3.3.0) | |RPostgreSQL | |0.4-1 |2016-05-08 |CRAN (R 3.3.0) | |RSQLite | |1.0.0 |2014-10-25 |CRAN (R 3.3.0) | |testthat | |1.0.2.9000 |2016-06-16 |Github (hadley/testthat@d3e20b9) | |tibble | |1.0-12 |2016-06-23 |Github (hadley/tibble@1e5b140) |
297 packages
Maintainer: Markus Belfrage markus.belfrage@gmail.com
0 errors | 0 warnings | 0 notes
Maintainer: Thibaut Jombart thibautjombart@gmail.com
0 errors | 0 warnings | 0 notes
Maintainer: Thomas Mailund mailund@birc.au.dk Bug reports: https://github.com/mailund/admixture_graph/issues
0 errors | 0 warnings | 0 notes
Maintainer: Yifan "Ethan" Xu ethan.yifanxu@gmail.com Bug reports: https://github.com/ethanyxu/ADPclust/issues
0 errors | 0 warnings | 0 notes
Maintainer: Imanuel Costigan i.costigan@me.com
1 error | 0 warnings | 0 notes
checking whether package ‘aemo’ can be installed ... ERROR
Installation failed.
See ‘/Users/hadley/Documents/dplyr/dplyr/revdep/checks/aemo.Rcheck/00install.out’ for details.
Maintainer: Henrik Singmann singmann+afex@gmail.com
0 errors | 0 warnings | 0 notes
Maintainer: Jason Vander Heiden jason.vanderheiden@yale.edu Bug reports: https://bitbucket.org/kleinstein/alakazam/issues
0 errors | 1 warning | 0 notes
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
Loading required package: ggplot2
Quitting from lines 78-109 (AminoAcids-Vignette.Rmd)
Error: processing vignette 'AminoAcids-Vignette.Rmd' failed with diagnostics:
could not find function "starts_with"
Execution halted
Maintainer: Eric Persson expersso5@gmail.com Bug reports: http://github.com/expersso/ameco/issues
0 errors | 0 warnings | 1 note
checking installed package size ... NOTE
installed size is 15.3Mb
sub-directories of 1Mb or more:
data 15.2Mb
Maintainer: Przemyslaw Biecek przemyslaw.biecek@gmail.com Bug reports: https://github.com/pbiecek/archivist/issues
0 errors | 0 warnings | 0 notes
Maintainer: Matthew Kay mjskay@uw.edu Bug reports: https://github.com/mjskay/ARTool/issues/new
0 errors | 0 warnings | 0 notes
Maintainer: Richard Cotton richierocks@gmail.com Bug reports: https://bitbucket.org/richierocks/assertive.types/issues
0 errors | 0 warnings | 0 notes
Maintainer: Tony Fischetti tony.fischetti@gmail.com Bug reports: https://github.com/tonyfischetti/assertr/issues
2 errors | 0 warnings | 1 note
checking examples ... ERROR
Running examples in ‘assertr-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: maha_dist
> ### Title: Computes mahalanobis distance for each row of data frame
> ### Aliases: maha_dist
>
> ### ** Examples
... 33 lines ...
>
> library(magrittr) # for piping operator
>
> # using every column from mtcars, compute mahalanobis distance
> # for each observation, and ensure that each distance is within 10
> # median absolute deviations from the median
> mtcars %>%
+ insist_rows(maha_dist, within_n_mads(10), everything())
Error in eval(expr, envir, enclos) : could not find function "everything"
Calls: %>% ... select_vars_ -> <Anonymous> -> lapply -> FUN -> eval -> eval
Execution halted
checking tests ... ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
1. Error: assert_rows returns data if verification passes (@test-assertions.R#189)
2. Failure: assert_rows raises error if verification fails (@test-assertions.R#217)
3. Failure: assert_rows raises error if verification fails (@test-assertions.R#221)
4. Failure: assert_rows raises *custom error* if verification fails (@test-assertions.R#237)
5. Failure: assert_rows raises *custom error* if verification fails (@test-assertions.R#241)
6. Error: insist_rows returns data if verification passes (@test-assertions.R#377)
7. Failure: insist_rows raises error if verification fails (@test-assertions.R#391)
8. Failure: insist_rows raises error if verification fails (@test-assertions.R#393)
9. Failure: insist_rows raises *custom error* if verification fails (@test-assertions.R#414)
10. Failure: insist_rows raises *custom error* if verification fails (@test-assertions.R#416)
Error: testthat unit tests failed
Execution halted
checking R code for possible problems ... NOTE
maha_dist: no visible global function definition for ‘cov’
within_n_mads : <anonymous>: no visible global function definition for
‘mad’
within_n_mads : <anonymous>: no visible global function definition for
‘median’
within_n_sds : <anonymous>: no visible global function definition for
‘sd’
Undefined global functions or variables:
cov mad median sd
Consider adding
importFrom("stats", "cov", "mad", "median", "sd")
to your NAMESPACE file.
Maintainer: Alex Lishinski alexlishinski@gmail.com
0 errors | 0 warnings | 0 notes
Maintainer: Miller Zijie Zhu zijie.miller.zhu@gmail.com
0 errors | 0 warnings | 0 notes
Maintainer: Michael Braun braunm@smu.edu
0 errors | 0 warnings | 0 notes
Maintainer: Massimo Aria aria@unina.it
0 errors | 0 warnings | 0 notes
Maintainer: Hadley Wickham hadley@rstudio.com
1 error | 0 warnings | 0 notes
checking whether package ‘bigrquery’ can be installed ... ERROR
Installation failed.
See ‘/Users/hadley/Documents/dplyr/dplyr/revdep/checks/bigrquery.Rcheck/00install.out’ for details.
Maintainer: Scott Chamberlain myrmecocystus@gmail.com Bug reports: https://github.com/ropensci/binomen/issues
0 errors | 0 warnings | 0 notes
Maintainer: Alberto Garre garre.alberto@gmail.com
0 errors | 0 warnings | 0 notes
Maintainer: Hajk-Georg Drost hgd23@cam.ac.uk Bug reports: https://github.com/HajkD/biomartr/issues
1 error | 0 warnings | 0 notes
checking package dependencies ... ERROR
Packages required but not available: ‘biomaRt’ ‘Biostrings’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: Yann Abraham yann.abraham@gmail.com Bug reports: https://github.com/yannabraham/bodenmiller/issues
0 errors | 0 warnings | 1 note
checking installed package size ... NOTE
installed size is 8.9Mb
sub-directories of 1Mb or more:
data 8.7Mb
Maintainer: Sacha Epskamp mail@sachaepskamp.com
0 errors | 0 warnings | 0 notes
Maintainer: Brendan Rocks rocks.brendan@gmail.com Bug reports: https://github.com/brendan-R/boxr/issues
0 errors | 0 warnings | 0 notes
Maintainer: David Robinson admiral.david@gmail.com Bug reports: http://github.com/dgrtwo/broom/issues
2 errors | 0 warnings | 0 notes
checking examples ... ERROR
Running examples in ‘broom-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: survfit_tidiers
> ### Title: tidy survival curve fits
> ### Aliases: glance.survfit survfit_tidiers tidy.survfit
>
> ### ** Examples
... 48 lines ...
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
Error: Unknown column 'median'
Execution halted
checking tests ... ERROR
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
4: identical(as.vector(object), TRUE) at /private/tmp/RtmpjWok2u/devtools5ce3473eae2e/hadley-testthat-d3e20b9/R/expectation.R:112
5: as.vector(object)
6: augmented$disp
7: `$.tbl_df`(augmented, disp)
8: stopc("Unknown column '", i, "'") at /private/tmp/RtmpxqBRhg/devtools1785e2d679c7f/hadley-tibble-1e5b140/R/tbl-df.r:37
9: stop(..., call. = FALSE, domain = NA) at /private/tmp/RtmpxqBRhg/devtools1785e2d679c7f/hadley-tibble-1e5b140/R/utils.r:63
testthat results ================================================================
OK: 490 SKIPPED: 0 FAILED: 1
1. Error: rowwise tidiers can be applied to sub-models (@test-rowwise.R#21)
Error: testthat unit tests failed
Execution halted
Maintainer: Duncan Lee Duncan.Lee@glasgow.ac.uk
0 errors | 0 warnings | 0 notes
Maintainer: Douglas Galagate galagated@gmail.com
0 errors | 0 warnings | 0 notes
Maintainer: Edwin de Jonge edwindjonge@gmail.com Bug reports: https://github.com/edwindj/cbsodataR/issues
0 errors | 0 warnings | 0 notes
Maintainer: Bob Rudis bob@rudis.net Bug reports: https://github.com/hrbrmstr/cdcfluview/issues
0 errors | 0 warnings | 0 notes
Maintainer: Greg Macfarlane gregmacfarlane@gmail.com
0 errors | 0 warnings | 0 notes
Maintainer: Michel Lang michellang@gmail.com Bug reports: https://github.com/mllg/checkmate/issues
0 errors | 0 warnings | 0 notes
Maintainer: Ari Lamstein arilamstein@gmail.com Bug reports: https://github.com/arilamstein/choroplethr/issues
0 errors | 0 warnings | 0 notes
Maintainer: Matthew Pennell mwpennell@gmail.com Bug reports: http://www.github.com/ropensci/chromer/issues/new
0 errors | 0 warnings | 2 notes
checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
checking R code for possible problems ... NOTE
parse_counts: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
na.omit
Consider adding
importFrom("stats", "na.omit")
to your NAMESPACE file.
Maintainer: Edwin de Jonge edwindjonge@gmail.com Bug reports: https://github.com/edwindj/chunked/issues
1 error | 0 warnings | 0 notes
checking tests ... ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
incorrect number of dimensions
1: write_chunkwise(iris2, tmp, row.names = FALSE) at testthat/test-write.R:29
2: write_chunkwise.tbl_sql(iris2, tmp, row.names = FALSE)
3: utils::write.table(h[0, ], file = file, col.names = col.names, row.names = row.names,
sep = sep, dec = dec, ...)
4: is.data.frame(x)
testthat results ================================================================
OK: 26 SKIPPED: 0 FAILED: 1
1. Error: write_chunkwise to db works (@test-write.R#29)
Error: testthat unit tests failed
Execution halted
Maintainer: Bill Venables Bill.Venables@gmail.com
0 errors | 0 warnings | 0 notes
Maintainer: Matthew B. Jones jones@nceas.ucsb.edu Bug reports: https://github.com/laurenmh/codyn/issues
0 errors | 0 warnings | 0 notes
Maintainer: Fong Chun Chan fongchunchan@gmail.com Bug reports: https://github.com/tinyheero/cofeatureR/issues
0 errors | 0 warnings | 0 notes
Maintainer: Kaiyin Zhong kindlychung@gmail.com Bug reports: https://bitbucket.org/kindlychung/collapsabel2/issues
0 errors | 0 warnings | 0 notes
Maintainer: Max Leiserson mdml@cs.brown.edu
0 errors | 0 warnings | 0 notes
Maintainer: Alex Joseph alexsanjoseph@gmail.com
0 errors | 0 warnings | 0 notes
Maintainer: Sergio Oller Moreno sergioller@gmail.com Bug reports: http://github.com/zeehio/condformat/issues
2 errors | 0 warnings | 0 notes
checking examples ... ERROR
Running examples in ‘condformat-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: show_columns
> ### Title: Selects the variables to be printed
> ### Aliases: show_columns show_columns_
>
> ### ** Examples
... 94 lines ...
<td style='border-bottom: 2px solid grey; text-align: left;'>6</td>
<td style='border-bottom: 2px solid grey; text-align: center;'>5.4</td>
<td style='border-bottom: 2px solid grey; text-align: center;'>3.9</td>
<td style='border-bottom: 2px solid grey; text-align: center;'>setosa</td>
</tr>
</tbody>
</table>> condformat(x) + show_columns(starts_with("Petal"), Species)
Error in eval(expr, envir, enclos) :
could not find function "starts_with"
Calls: <Anonymous> ... <Anonymous> -> <Anonymous> -> lapply -> FUN -> eval -> eval
Execution halted
checking tests ... ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
1. Error: knitr returns an HTML table (@test_rendering.R#18)
2. Error: rule_fill_discrete works (@test_rule_fill_discrete.R#14)
3. Error: rule_fill_discrete lock cells (@test_rule_fill_discrete.R#39)
4. Error: rule_fill_discrete_ works (@test_rule_fill_discrete.R#67)
5. Error: rule_fill_gradient works (@test_rule_fill_gradient.R#12)
6. Error: rule_fill_gradient2 works (@test_rule_fill_gradient.R#24)
7. Error: show_column works (@test_show.R#12)
8. Error: show_column_ works (@test_show.R#24)
9. Error: show_column works with custom names (@test_show.R#36)
1. ...
Error: testthat unit tests failed
Execution halted
Maintainer: Christopher Gandrud christopher.gandrud@gmail.com Bug reports: https://github.com/christophergandrud/coreSim/issues
0 errors | 0 warnings | 0 notes
Maintainer: Brooke Anderson brooke.anderson@colostate.edu Bug reports: https://github.com/geanders/countytimezones/issues
0 errors | 0 warnings | 0 notes
Maintainer: Devin S. Johnson devin.johnson@noaa.gov
0 errors | 0 warnings | 0 notes
Maintainer: Tinniam V Ganesh tvganesh.85@gmail.com Bug reports: https://github.com/tvganesh/cricketr/issues
0 errors | 0 warnings | 0 notes
Maintainer: Joe Thorley joe@poissonconsulting.ca
0 errors | 0 warnings | 0 notes
Maintainer: Christopher Gandrud christopher.gandrud@gmail.com Bug reports: https://github.com/christophergandrud/DataCombine/issues
0 errors | 0 warnings | 0 notes
Maintainer: Ryan Hafen rhafen@gmail.com
0 errors | 0 warnings | 1 note
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘Rhipe’
Maintainer: Imanuel Costigan i.costigan@me.com Bug reports: https://github.com/imanuelcostigan/dataonderivatives/issues
0 errors | 0 warnings | 0 notes
Maintainer: Laura DeCicco ldecicco@usgs.gov Bug reports: https://github.com/USGS-R/dataRetrieval/issues
0 errors | 0 warnings | 0 notes
Maintainer: Brandon Taylor brandon.taylor221@gmail.com
0 errors | 1 warning | 0 notes
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
recursively.
_E_x_a_m_p_l_e_s:
step = dataStepClass$new()
frame = data.frame(x = 1:10)
... 8 lines ...
}
stairs()
step$results
Quitting from lines 55-84 (datastepping.Rmd)
Error: processing vignette 'datastepping.Rmd' failed with diagnostics:
incorrect length (2), expecting: 10
Execution halted
Maintainer: Dean Attali daattali@gmail.com Bug reports: https://github.com/daattali/ddpcr/issues
2 errors | 1 warning | 0 notes
checking examples ... ERROR
Running examples in ‘ddpcr-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: calculate_negative_freqs
> ### Title: Calculate negative frequencies in whole plate
> ### Aliases: calculate_negative_freqs
> ### Keywords: internal
>
> ### ** Examples
>
> file <- system.file("sample_data", "small", "analyzed_pnpp.rds", package = "ddpcr")
> plate <- load_plate(file)
> plate %>% calculate_negative_freqs %>%
+ well_info(wells_success(plate), "negative_freq")
Error in eval(expr, envir, enclos) : could not find function "one_of"
Calls: %>% ... select_vars_ -> <Anonymous> -> lapply -> FUN -> eval -> eval
Execution halted
checking tests ... ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
Attaching package: 'ddpcr'
The following object is masked from 'package:stats':
step
>
> test_check("ddpcr")
Error: ddpcr: there was a problem reading one or more of the data files
testthat results ================================================================
OK: 0 SKIPPED: 0 FAILED: 0
Execution halted
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
Quitting from lines 205-213 (extend.Rmd)
Error: processing vignette 'extend.Rmd' failed with diagnostics:
ddpcr: there was a problem reading one or more of the data files
Execution halted
Maintainer: John Reid john.reid@mrc-bsu.cam.ac.uk
0 errors | 1 warning | 0 notes
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
Joining, by = c("cell", "capture")
Have 35 cells after filtering
Joining, by = "cell"
Have 20 genes after filtering
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
... 8 lines ...
In file included from /Users/hadley/R-revdep/StanHeaders/include/src/stan/io/dump.hpp:11:
In file included from /Users/hadley/R-revdep/StanHeaders/include/src/stan/io/validate_zero_buf.hpp:4:
/Users/hadley/R-revdep/BH/include/boost/lexical_cast/bad_lexical_cast.hpp:33:54: error: redefinition of 'bad_lexical_cast'
class __attribute__((__visibility__("default"))) bad_lexical_cast :
^
/usr/local/include/boost/lexical_cast.hpp:75:54: note: previous definition is here
class __attribute__((__visibility__("default"))) bad_lexical_cast :
^
1 error generated.
make: *** [file6da35a13b51f.o] Error 1
Execution halted
Maintainer: James Ware j.ware@imperial.ac.uk Bug reports: http://github.com/jamesware/denovolyzeR/issues
0 errors | 0 warnings | 0 notes
Maintainer: Zygmunt Zawadzki zawadzkizygmunt@gmail.com
0 errors | 0 warnings | 0 notes
Maintainer: Paul Hendricks paul.hendricks.2013@owu.edu Bug reports: https://github.com/paulhendricks/describer/issues
1 error | 0 warnings | 0 notes
checking tests ... ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
expect_equal( strings_addresses(names(df)) , strings_addresses(names(df4)) )
~^
tests/testthat/utf-8.R:17:44: style: Commas should never have a space before.
expect_equal( strings_addresses(names(df)) , strings_addresses(names(gdf4)) )
~^
testthat results ================================================================
OK: 7 SKIPPED: 0 FAILED: 1
1. Failure: Package Style (@test-styling.R#4)
Error: testthat unit tests failed
Execution halted
Maintainer: Hasanthi A. Pathberiya hasanthi@sjp.ac.lk
0 errors | 0 warnings | 0 notes
Maintainer: Derek Corcoran derek.corcoran.barrios@gmail.com
0 errors | 0 warnings | 0 notes
Maintainer: Bob Rudis bob@rudis.net
0 errors | 0 warnings | 0 notes
Maintainer: Yue Hu yue-hu-1@uiowa.edu Bug reports: https://github.com/fsolt/dotwhisker/issues
1 error | 1 warning | 0 notes
checking examples ... ERROR
Running examples in ‘dotwhisker-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: small_multiple
> ### Title: Generate a 'Small Multiple' Plot of Regression Results
> ### Aliases: small_multiple
>
> ### ** Examples
... 55 lines ...
+ theme(axis.text.x = element_text(angle = 45, hjust = 1),
+ legend.position=c(0, 0), legend.justification=c(0, 0),
+ legend.title = element_text(size=9),
+ legend.background = element_rect(color="gray90"),
+ legend.margin = unit(-3, "pt"),
+ legend.key.size = unit(10, "pt")) +
+ scale_colour_hue(name = "Transmission",
+ breaks = c(0, 1),
+ labels = c("Automatic", "Manual"))
Error: cannot convert object to a data frame
Execution halted
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
Warning: Deprecated, use tibble::rownames_to_column() instead.
Loading required package: sandwich
Loading required package: lmtest
Loading required package: zoo
Attaching package: 'zoo'
... 8 lines ...
The following object is masked from 'package:dplyr':
select
Loading required package: betareg
Warning: Deprecated, use tibble::rownames_to_column() instead.
Quitting from lines 168-211 (dotwhisker-vignette.Rmd)
Error: processing vignette 'dotwhisker-vignette.Rmd' failed with diagnostics:
no applicable method for 'group_by_' applied to an object of class "c('matrix', 'list')"
Execution halted
Maintainer: Brandon Taylor brandon.taylor221@gmail.com Bug reports: https://github.com/bramtayl/easyformatr/issues
2 errors | 1 warning | 0 notes
checking examples ... ERROR
Running examples in ‘easyformatr-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: easy_format
> ### Title: Easily build format strings
> ### Aliases: easy_format
>
> ### ** Examples
>
> easy_format(year, month, day, integer, octal, double)
Error in eval(expr, envir, enclos) : could not find function "one_of"
Calls: easy_format ... select_vars_ -> <Anonymous> -> lapply -> FUN -> eval -> eval
Execution halted
checking tests ... ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
53: select_vars_(names(.data), dots) at /Users/hadley/Documents/dplyr/dplyr/R/dataframe.R:97
54: lazyeval::lazy_eval(args, names_list) at /Users/hadley/Documents/dplyr/dplyr/R/select-vars.R:69
55: lapply(x, lazy_eval, data = data) at /private/tmp/RtmpBZGgmu/devtools500b57ff4370/hadley-lazyeval-c155c3d/R/lazy-eval.R:21
56: FUN(X[[i]], ...)
57: eval(x$expr, data, x$env) at /private/tmp/RtmpBZGgmu/devtools500b57ff4370/hadley-lazyeval-c155c3d/R/lazy-eval.R:27
58: eval(expr, envir, enclos)
testthat results ================================================================
OK: 7 SKIPPED: 0 FAILED: 1
1. Error: easy_format (@test.R#48)
Error: testthat unit tests failed
Execution halted
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
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
Quitting from lines 39-40 (easyformatr.Rmd)
Error: processing vignette 'easyformatr.Rmd' failed with diagnostics:
object 'data_frame' not found
Execution halted
Maintainer: Eric Persson expersso5@gmail.com
0 errors | 0 warnings | 0 notes
Maintainer: Karthik Ram karthik.ram@gmail.com Bug reports: https://github.com/ropensci/ecoengine/issues
0 errors | 0 warnings | 0 notes
Maintainer: Gert Janssenswillen gert.janssenswillen@uhasselt.be
0 errors | 1 warning | 0 notes
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
Attaching package: 'edeaR'
The following object is masked from 'package:utils':
timestamp
Quitting from lines 92-94 (descriptives.Rmd)
Error: processing vignette 'descriptives.Rmd' failed with diagnostics:
Can not automatically convert from numeric to factor in column "length".
Execution halted
Maintainer: Ben Marwick benmarwick@gmail.com
0 errors | 0 warnings | 0 notes
Maintainer: Philippe Massicotte pm@bios.au.dk Bug reports: https://github.com/PMassicotte/eemR/issues
0 errors | 0 warnings | 0 notes
Maintainer: Andrew Zammit-Mangion andrewzm@gmail.com
0 errors | 0 warnings | 1 note
checking R code for possible problems ... NOTE
.gdf : find_loss: no visible global function definition for ‘rnorm’
.p.values : <anonymous>: no visible global function definition for
‘pnorm’
.relist.dwt: no visible global function definition for ‘relist’
.relist.dwt: no visible global function definition for ‘as’
.std.wav.coeff : <anonymous>: no visible global function definition for
‘mad’
regrid: no visible global function definition for ‘predict’
regrid: no visible global function definition for ‘var’
regrid: no visible global function definition for ‘medpolish’
Undefined global functions or variables:
as mad medpolish pnorm predict relist rnorm var
Consider adding
importFrom("methods", "as")
importFrom("stats", "mad", "medpolish", "pnorm", "predict", "rnorm",
"var")
importFrom("utils", "relist")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Maintainer: Marco Bascietto marco.bascietto@crea.gov.it
0 errors | 0 warnings | 0 notes
Maintainer: Jordan Mackie jmackie@protonmail.com
1 error | 1 warning | 0 notes
checking examples ... ERROR
Running examples in ‘elpatron-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: clean_bikedata
> ### Title: Clean raw cycling device data.
> ### Aliases: clean_bikedata
>
> ### ** Examples
>
> ride_file <- system.file("extdata/lufbra.fit", package = "elpatron")
>
> parsed_ride <- import_ride(ride_file, make_laps = TRUE)
Error: Length of logical index vector must be 1 or 18, got: 17
Execution halted
checking Rd cross-references ... WARNING
Missing link or links in documentation object 'pipe.Rd':
‘[dplyr]{chain}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
Maintainer: Christofer Backlin emil@christofer.backlin.se Bug reports: https://github.com/Molmed/emil/issues
0 errors | 0 warnings | 0 notes
Maintainer: Raphael Winkelmann raphael@phonetik.uni-muenchen.de Bug reports: https://github.com/IPS-LMU/emuR/issues
0 errors | 0 warnings | 0 notes
Maintainer: James Curley jc3181@columbia.edu
0 errors | 0 warnings | 0 notes
Maintainer: Scott Chamberlain myrmecocystus@gmail.com Bug reports: https://github.com/ropengov/enigma/issues
0 errors | 0 warnings | 0 notes
Maintainer: Hiroaki Yutani yutani.ini@gmail.com
0 errors | 0 warnings | 0 notes
Maintainer: Ben Baumer ben.baumer@gmail.com Bug reports: https://github.com/beanumber/etl/issues
0 errors | 0 warnings | 0 notes
Maintainer: Lahti Leo louhos@googlegroups.com Bug reports: https://github.com/ropengov/eurostat/issues
0 errors | 0 warnings | 0 notes
Maintainer: Julien Barnier julien.barnier@ens-lyon.fr Bug reports: https://github.com/juba/explor/issues
0 errors | 0 warnings | 0 notes
Maintainer: Simon Barthelme simon.barthelme@gipsa-lab.fr
0 errors | 0 warnings | 0 notes
Maintainer: Jacob Dink jacobwdink@gmail.com Bug reports: https://github.com/jwdink/eyetrackingR/issues
0 errors | 0 warnings | 0 notes
Maintainer: Zhian N. Kamvar kamvarz@science.oregonstate.edu Bug reports: https://github.com/grunwaldlab/ezec/issues
0 errors | 0 warnings | 0 notes
Maintainer: Hao Zhu haozhu@hsl.harvard.edu
0 errors | 0 warnings | 0 notes
Maintainer: Francois Husson francois.husson@agrocampus-ouest.fr
0 errors | 0 warnings | 0 notes
Maintainer: Hadley Wickham hadley@rstudio.com Bug reports: https://github.com/wesm/feather/issues
0 errors | 0 warnings | 0 notes
Maintainer: Seward Lee sewardlee337@gmail.com
0 errors | 0 warnings | 0 notes
Maintainer: Niraj Juneja njuneja@gmail.com
0 errors | 0 warnings | 0 notes
Maintainer: Gustavo Carvalho gustavo.bio@gmail.com Bug reports: http://www.github.com/gustavobio/flora/issues
0 errors | 0 warnings | 0 notes
Maintainer: Nick Kennedy r@nick-kennedy.com
0 errors | 0 warnings | 0 notes
Maintainer: Bill Venables bill.venables@gmail.com
0 errors | 0 warnings | 0 notes
Maintainer: Emilio Torres-Manzanera torres@uniovi.es
0 errors | 0 warnings | 1 note
checking R code for possible problems ... NOTE
.corfreq: no visible global function definition for ‘complete.cases’
.covfreq: no visible global function definition for ‘complete.cases’
.hclustvfreq: no visible global function definition for
‘complete.cases’
.quantilefreq : <anonymous>: no visible global function definition for
‘approx’
coef.biglmfreq: no visible global function definition for ‘coef’
predict.biglmfreq: no visible global function definition for ‘predict’
predict.lmfreq: no visible global function definition for ‘predict’
summary.lmfreq: no visible global function definition for ‘coef’
summary.lmfreq: no visible global function definition for ‘pt’
summary.lmfreq: no visible global function definition for ‘AIC’
update.biglmfreq: no visible global function definition for ‘update’
Undefined global functions or variables:
AIC approx coef complete.cases predict pt update
Consider adding
importFrom("stats", "AIC", "approx", "coef", "complete.cases",
"predict", "pt", "update")
to your NAMESPACE file.
Maintainer: Derek Ogle derek@derekogle.com Bug reports: https://github.com/droglenc/FSA/issues
0 errors | 0 warnings | 1 note
checking Rd cross-references ... NOTE
Packages unavailable to check Rd xrefs: ‘alr3’, ‘prettyR’, ‘RMark’, ‘asbio’, ‘PMCMR’, ‘pgirmess’, ‘agricolae’
Maintainer: 'Hadley Wickham' h.wickham@gmail.com
0 errors | 0 warnings | 0 notes
Maintainer: Brooke Anderson brooke.anderson@colostate.edu
0 errors | 0 warnings | 0 notes
Maintainer: David Robinson drobinson@stackoverflow.com
0 errors | 0 warnings | 0 notes
Maintainer: Jennifer Bryan jenny@stat.ubc.ca Bug reports: https://github.com/jennybc/gapminder/issues
0 errors | 0 warnings | 0 notes
Maintainer: Eric Reed reeder@bu.edu
1 error | 1 warning | 3 notes
checking examples ... ERROR
Running examples in ‘GenCAT-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GenCAT
> ### Title: Running GenCAT
> ### Aliases: GenCAT
> ### Keywords: ~kwd1 ~kwd2
>
... 15 lines ...
SNP effect_allele other_allele testStat chr position class
17232 rs9572807 C T -0.3014771 13 72423959 DACH1
24151 rs4389009 G A -1.4443860 13 99193519 STK24
37178 rs7151730 T A 0.1387317 14 33531585 NPAS3
58941 rs1076958 G A 2.0597766 14 91131857 TTC7B
13089 rs7987481 G A -1.0024210 13 47318950 LRCH1
58302 rs411064 G A 0.2132412 14 90008860 FOXN3
>
> library(snpStats)
Error in library(snpStats) : there is no package called ‘snpStats’
Execution halted
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
Loading required package: dplyr
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
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
Loading required package: ggplot2
Quitting from lines 62-69 (GenCAT-vignette.Rmd)
Error: processing vignette 'GenCAT-vignette.Rmd' failed with diagnostics:
unable to find required package 'snpStats'
Execution halted
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘snpStats’
checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘snpStats’
checking data for non-ASCII characters ... NOTE
Error in .requirePackage(package) :
unable to find required package 'snpStats'
Calls: <Anonymous> ... .extendsForS3 -> extends -> getClassDef -> .requirePackage
Execution halted
Maintainer: Lincoln Mullen lincoln@lincolnmullen.com Bug reports: https://github.com/ropensci/gender/issues
0 errors | 0 warnings | 1 note
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘genderdata’
Maintainer: Samantha Tyner sctyner@iastate.edu Bug reports: https://github.com/sctyner/geomnet/issues
0 errors | 0 warnings | 0 notes
Maintainer: Bob Rudis bob@rudis.net Bug reports: https://github.com/hrbrmstr/ggalt/issues
0 errors | 0 warnings | 0 notes
Maintainer: Masaaki Horikoshi sinhrks@gmail.com
0 errors | 0 warnings | 1 note
checking installed package size ... NOTE
installed size is 5.3Mb
sub-directories of 1Mb or more:
doc 4.9Mb
Maintainer: David Kahle david.kahle@gmail.com Bug reports: https://github.com/dkahle/ggmap/issues
0 errors | 0 warnings | 0 notes
Maintainer: Xavier Fernández i Marín xavier.fim@gmail.com Bug reports: https://github.com/xfim/ggmcmc/issues
1 error | 0 warnings | 0 notes
checking examples ... ERROR
Running examples in ‘ggmcmc-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggs_caterpillar
> ### Title: Caterpillar plot with thick and thin CI
> ### Aliases: ggs_caterpillar
>
> ### ** Examples
>
> data(linear)
> ggs_caterpillar(ggs(s))
> ggs_caterpillar(list(A=ggs(s), B=ggs(s))) # silly example duplicating the same model
Error: Unknown column 'description'
Execution halted
Maintainer: Pedro J. Aphalo pedro.aphalo@helsinki.fi Bug reports: https://bitbucket.org/aphalo/ggpmisc
0 errors | 0 warnings | 0 notes
Maintainer: John Ehrlinger john.ehrlinger@gmail.com Bug reports: https://github.com/ehrlinger/ggRandomForests/issues
0 errors | 0 warnings | 1 note
checking installed package size ... NOTE
installed size is 5.1Mb
sub-directories of 1Mb or more:
data 2.6Mb
doc 2.1Mb
Maintainer: Eugene Dubossarsky eugene@presciient.com Bug reports: https://github.com/cargomoose/raptR/issues
0 errors | 0 warnings | 0 notes
Maintainer: Pedro J. Aphalo pedro.aphalo@helsinki.fi Bug reports: https://bitbucket.org/aphalo/ggspectra
1 error | 1 warning | 0 notes
checking examples ... ERROR
Running examples in ‘ggspectra-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggspectra-package
> ### Title: Extensions to 'ggplot2' for Radiation Spectra
> ### Aliases: ggspectra ggspectra-package
>
> ### ** Examples
... 17 lines ...
+ stat_peaks(span = 21, geom = "point", colour = "red") +
+ stat_peaks(span = 51, geom = "text", colour = "red", vjust = -0.3,
+ label.fmt = "%3.0f nm")
>
> ggplot(sun.spct, aes(w.length, s.e.irrad)) + geom_line() +
+ stat_color() + scale_color_identity()
>
> plot(sun.spct)
> plot(polyester.spct, UV_bands(), range = UV())
Error: evaluation nested too deeply: infinite recursion / options(expressions=)?
Execution halted
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
Error: processing vignette 'user-guide.Rmd' failed with diagnostics:
evaluation nested too deeply: infinite recursion / options(expressions=)?
Execution halted
Maintainer: Winston Chang winston@rstudio.com
1 error | 0 warnings | 1 note
checking tests ... ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
[8] 7 - 2 == 5
[9] 7 - 2 == 5
...
testthat results ================================================================
OK: 444 SKIPPED: 0 FAILED: 1
1. Failure: Automatic width (@test-compute-bin.r#143)
Error: testthat unit tests failed
In addition: Warning message:
In bind_rows_(x, .id) : Unequal factor levels: coercing to character
Execution halted
checking R code for possible problems ... NOTE
adjust_breaks: no visible global function definition for ‘median’
bin_params.POSIXct: no visible global function definition for ‘is’
bin_vector.POSIXct: no visible global function definition for ‘is’
combine_data_props: no visible global function definition for
‘setNames’
combine_data_props : <anonymous>: no visible global function definition
for ‘setNames’
compute_boxplot.data.frame: no visible global function definition for
‘quantile’
... 24 lines ...
‘packageVersion’
Undefined global functions or variables:
complete.cases formula is median na.omit packageVersion predict qt
quantile runif setNames terms
Consider adding
importFrom("methods", "is")
importFrom("stats", "complete.cases", "formula", "median", "na.omit",
"predict", "qt", "quantile", "runif", "setNames", "terms")
importFrom("utils", "packageVersion")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Maintainer: Scott Chamberlain myrmecocystus@gmail.com Bug reports: http://www.github.com/ropensci/gistr/issues
0 errors | 0 warnings | 0 notes
Maintainer: Jirka Lewandowski jirka.lewandowski@wzb.eu Bug reports: http://gitlab.points-of-interest.cc/points-of-interest/gitlabr/ issues/
0 errors | 0 warnings | 0 notes
Maintainer: Ivo Ugrina ivo@iugrina.com Bug reports: https://github.com/iugrina/glycanr/issues
2 errors | 0 warnings | 1 note
checking examples ... ERROR
Running examples in ‘glycanr-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: quantilenorm
> ### Title: Quantile Normalization of glycan data
> ### Aliases: quantilenorm
>
> ### ** Examples
>
> data(mpiu)
> mpiun <- quantilenorm(mpiu)
Error in quantilenorm(mpiu) :
Unable to proceed since package preprocessCore from
BioConductor is not available on this system. This
package is a prerequisite to use the quantilenorm function!
Execution halted
checking tests ... ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Error in quantilenorm(mpiu, transpose = TRUE) :
Unable to proceed since package preprocessCore from
BioConductor is not available on this system. This
package is a prerequisite to use the quantilenorm function!
Calls: test_check ... force -> source_file -> eval -> eval -> quantilenorm
testthat results ================================================================
OK: 5 SKIPPED: 0 FAILED: 0
Execution halted
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘preprocessCore’
Maintainer: Jennifer Bryan jenny@stat.ubc.ca Bug reports: https://github.com/jennybc/googlesheets/issues
0 errors | 0 warnings | 0 notes
Maintainer: John Coene jcoenep@gmail.com Bug reports: https://github.com/JohnCoene/graphTweets/issues
0 errors | 0 warnings | 0 notes
Maintainer: Max Gordon max@gforge.se
0 errors | 0 warnings | 1 note
checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘rmeta’
Maintainer: Kathleen sprouffske sprouffske@gmail.com Bug reports: https://github.com/sprouffske/growthcurver/issues
0 errors | 0 warnings | 0 notes
Maintainer: Adam Sparks adamhsparks@gmail.com Bug reports: https://github.com/adamhsparks/GSODR/issues
0 errors | 0 warnings | 0 notes
Maintainer: Dirk Eddelbuettel edd@debian.org
0 errors | 0 warnings | 0 notes
Maintainer: David Robinson admiral.david@gmail.com Bug reports: http://github.com/ropenscilabs/gutenbergr/issues
2 errors | 0 warnings | 0 notes
checking examples ... ERROR
Running examples in ‘gutenbergr-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gutenberg_strip
> ### Title: Strip header and footer content from a Project Gutenberg book
> ### Aliases: gutenberg_strip
>
> ### ** Examples
... 10 lines ...
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
> book <- gutenberg_works(title == "Pride and Prejudice") %>%
+ gutenberg_download(strip = FALSE)
Determining mirror for Project Gutenberg from http://www.gutenberg.org/robot/harvest
Using mirror http://www.gutenberg.lib.md.us
Error: Unknown column 'gutenberg_id'
Execution halted
checking tests ... ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
7: `$.tbl_df`(w_de, language)
8: stopc("Unknown column '", i, "'") at /private/tmp/RtmpxqBRhg/devtools1785e2d679c7f/hadley-tibble-1e5b140/R/tbl-df.r:37
9: stop(..., call. = FALSE, domain = NA) at /private/tmp/RtmpxqBRhg/devtools1785e2d679c7f/hadley-tibble-1e5b140/R/utils.r:63
testthat results ================================================================
OK: 31 SKIPPED: 0 FAILED: 4
1. Error: Can download books from a data frame with gutenberg_id column (@test-download.R#40)
2. Error: gutenberg_works does appropriate filtering by default (@test-metadata.R#8)
3. Error: gutenberg_works takes filtering conditions (@test-metadata.R#17)
4. Error: gutenberg_works does appropriate filtering by language (@test-metadata.R#23)
Error: testthat unit tests failed
Execution halted
Maintainer: Hadley Wickham hadley@rstudio.com Bug reports: https://github.com/hadley/haven/issues
1 error | 0 warnings | 1 note
checking examples ... ERROR
Running examples in ‘haven-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: read_sas
> ### Title: Read SAS files.
> ### Aliases: read_sas
>
> ### ** Examples
>
> read_sas("http://crn.cancer.gov/resources/ctcodes-procedures.sas7bdat")
Error in download.file(path, tmp, quiet = TRUE, mode = "wb") :
cannot open URL 'http://crn.cancer.gov/resources/ctcodes-procedures.sas7bdat'
Calls: read_sas -> df_parse_sas -> clean_path -> download.file
Execution halted
checking R code for possible problems ... NOTE
clean_path: no visible global function definition for ‘download.file’
Undefined global functions or variables:
download.file
Consider adding
importFrom("utils", "download.file")
to your NAMESPACE file.
Maintainer: Eric Persson expersso5@gmail.com Bug reports: https://github.com/expersso/hdr
0 errors | 0 warnings | 0 notes
Maintainer: Antoine Filipovic-Pierucci pierucci@gmail.com Bug reports: https://github.com/pierucci/heemod/issues
0 errors | 0 warnings | 0 notes
Maintainer: Joshua Kunst jbkunst@gmail.com Bug reports: https://github.com/jbkunst/highcharter/issues
0 errors | 0 warnings | 0 notes
Maintainer: Benjamin Nutter benjamin.nutter@gmail.com Bug reports: https://github.com/nutterb/HydeNet/issues
1 error | 0 warnings | 0 notes
checking package dependencies ... ERROR
Package required but not available: ‘graph’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: Nick Bond n.bond@griffith.edu.au
0 errors | 0 warnings | 0 notes
Maintainer: Matthew Lincoln matthew.d.lincoln@gmail.com Bug reports: https://github.com/mdlincoln/hypothesisr/issues
0 errors | 0 warnings | 0 notes
Maintainer: Dan Martin dpmartin42@gmail.com
0 errors | 0 warnings | 0 notes
Maintainer: Giulio Costantini costantinigiulio@gmail.com
1 error | 0 warnings | 0 notes
checking package dependencies ... ERROR
Package required but not available: ‘nem’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: Kyle Walker kyle.walker@tcu.edu
0 errors | 0 warnings | 0 notes
Maintainer: Simon Barthelme simon.barthelme@gipsa-lab.fr
1 error | 0 warnings | 0 notes
checking whether package ‘imager’ can be installed ... ERROR
Installation failed.
See ‘/Users/hadley/Documents/dplyr/dplyr/revdep/checks/imager.Rcheck/00install.out’ for details.
Maintainer: Anup Nair nairanup50695@gmail.com
0 errors | 0 warnings | 0 notes
Maintainer: Phil Chapman phil.chapman@cruk.manchester.ac.uk Bug reports: https://github.com/chapmandu2/IncucyteDRC/issues
0 errors | 0 warnings | 0 notes
Maintainer: Lincoln Mullen lincoln@lincolnmullen.com Bug reports: https://github.com/ropensci/internetarchive/issues
0 errors | 0 warnings | 0 notes
Maintainer: Bill Venables Bill.Venables@gmail.com
0 errors | 0 warnings | 0 notes
Maintainer: Julia Silge julia.silge@gmail.com Bug reports: https://github.com/juliasilge/janeaustenr/issues
0 errors | 0 warnings | 0 notes
Maintainer: Joseph Larmarange joseph@larmarange.net Bug reports: https://github.com/larmarange/labelled/issues
0 errors | 0 warnings | 2 notes
checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘memisc’
checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘memisc’
Maintainer: Jordan S Read jread@usgs.gov Bug reports: https://github.com/USGS-R/laketemps/issues
0 errors | 0 warnings | 0 notes
Maintainer: Lawrence Wu lwu@payoff.com
0 errors | 0 warnings | 0 notes
Maintainer: Kris Sankaran kriss1@stanford.edu
0 errors | 0 warnings | 1 note
checking R code for possible problems ... NOTE
AnalyticalOptim: no visible global function definition for ‘optim’
LLConstructor : LL: no visible global function definition for ‘dpois’
MixtureDensity: no visible global function definition for ‘glm’
MixtureDensity : f_hat: no visible global function definition for
‘predict’
NullDensity : f0: no visible global function definition for ‘dpois’
Undefined global functions or variables:
dpois glm optim predict
Consider adding
importFrom("stats", "dpois", "glm", "optim", "predict")
to your NAMESPACE file.
Maintainer: Bob Rudis bob@rudis.net
0 errors | 0 warnings | 0 notes
Maintainer: Enzo Jia enzo.jia@gmail.com
0 errors | 0 warnings | 0 notes
Maintainer: Brandon Taylor Brandon.Taylor221@gmail.com
0 errors | 0 warnings | 1 note
checking R code for possible problems ... NOTE
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.
Maintainer: Ben Baumer ben.baumer@gmail.com
0 errors | 0 warnings | 0 notes
Maintainer: Jirka Lewandowski jirka.lewandowski@wzb.eu Bug reports: https://github.com/ManifestoProject/manifestoR/issues
0 errors | 0 warnings | 0 notes
Maintainer: Craig Varrichio canthony427@gmail.com
0 errors | 0 warnings | 0 notes
Maintainer: Jonathan Callahan jonathan.s.callahan@gmail.com
0 errors | 0 warnings | 0 notes
Maintainer: Jared E. Knowles jknowles@gmail.com Bug reports: https://www.github.com/jknowles/merTools
0 errors | 0 warnings | 0 notes
Maintainer: Bob Rudis bob@rudis.net Bug reports: https://github.com/hrbrmstr/metricsgraphics/issues
0 errors | 0 warnings | 0 notes
Maintainer: Eliot Miller eliot.isaac@gmail.com Bug reports: https://github.com/eliotmiller/metricTester/issues
0 errors | 0 warnings | 0 notes
Maintainer: Kim-Anh Le Cao k.lecao@uq.edu.au Bug reports: mixomics@math.univ-toulouse.fr or https://bitbucket.org/klecao/package-mixomics/issues
0 errors | 0 warnings | 0 notes
Maintainer: Sacha Epskamp mail@sachaepskamp.com
0 errors | 0 warnings | 0 notes
Maintainer: Alex Stringer alex@alexstringer.ca
2 errors | 1 warning | 0 notes
checking examples ... ERROR
Running examples in ‘modellingTools-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: create_model_matrix
> ### Title: Create a usable model matrix from a data frame containing a mix
> ### of continuous and categorical variables
> ### Aliases: create_model_matrix
>
... 7 lines ...
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
Error: Each variable must have a unique name.
Problem variables: 'var1', 'var1', 'var1', 'var1'
Execution halted
checking tests ... ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(modellingTools)
>
> test_check("modellingTools")
Error: Each variable must have a unique name.
Problem variables: 'var1', 'var1', 'var1'
testthat results ================================================================
OK: 53 SKIPPED: 0 FAILED: 0
Execution halted
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
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
Quitting from lines 313-319 (modellingTools.Rmd)
Error: processing vignette 'modellingTools.Rmd' failed with diagnostics:
Each variable must have a unique name.
Problem variables: 'var1', 'var1', 'var1', 'var1', 'var1', 'var1', 'var1'
Execution halted
Maintainer: Vincent Bonhomme bonhomme.vincent@gmail.com Bug reports: https://github.com/vbonhomme/Momocs/issues
0 errors | 0 warnings | 0 notes
Maintainer: Hannes Muehleisen hannes@cwi.nl Bug reports: https://github.com/hannesmuehleisen/MonetDBLite/issues
0 errors | 0 warnings | 1 note
checking installed package size ... NOTE
installed size is 5.9Mb
sub-directories of 1Mb or more:
libs 5.7Mb
Maintainer: Philippe Veber philippe.veber@univ-lyon1.fr
1 error | 0 warnings | 0 notes
checking whether package ‘morse’ can be installed ... ERROR
Installation failed.
See ‘/Users/hadley/Documents/dplyr/dplyr/revdep/checks/morse.Rcheck/00install.out’ for details.
Maintainer: Randall Pruim rpruim@calvin.edu Bug reports: https://github.com/ProjectMOSAIC/mosaic/issues
0 errors | 0 warnings | 1 note
checking installed package size ... NOTE
installed size is 9.2Mb
sub-directories of 1Mb or more:
R 1.8Mb
doc 6.8Mb
Maintainer: Randall Pruim rpruim@calvin.edu
0 errors | 0 warnings | 0 notes
Maintainer: Phil Ferriere pferriere@hotmail.com Bug reports: http://www.github.com/philferriere/mscstexta4r/issues
0 errors | 0 warnings | 0 notes
Maintainer: Subramanyam Ravishankar subramanyam@systeminsights.com
1 error | 0 warnings | 0 notes
checking examples ... ERROR
Running examples in ‘mtconnectR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: map_gcode_mtc
> ### Title: Create a mapping between simulated and actual data
> ### Aliases: map_gcode_mtc
>
> ### ** Examples
>
> data("example_gcode_parsed") # Parsed gcode
> data("example_mtc_device_3") # MTCDevice object of actual log data
> simulated_gcode_data = na.omit(simulate_data_from_gcode(example_gcode_parsed,
+ start_time = 0, data_res = 0.1, data_type = "HH"))
Error in eval(expr, envir, enclos) : could not find function "one_of"
Calls: na.omit ... select_vars_ -> <Anonymous> -> lapply -> FUN -> eval -> eval
Execution halted
Maintainer: Justin Alford justin.alford@gmail.com Bug reports: https://github.com/alforj/muir/issues
0 errors | 0 warnings | 0 notes
Maintainer: Hajk-Georg Drost hgd23@cam.ac.uk Bug reports: https://github.com/HajkD/myTAI/issues
1 error | 0 warnings | 0 notes
checking package dependencies ... ERROR
Package required but not available: ‘edgeR’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: Eduardo Flores eduardo@enelmargen.org
0 errors | 0 warnings | 0 notes
Maintainer: Chayan Acharya chayan.acharya@farmbio.uu.se
0 errors | 0 warnings | 0 notes
Maintainer: Nicholas Cooper nick.cooper@cimr.cam.ac.uk
0 errors | 0 warnings | 3 notes
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘BiocInstaller’
checking R code for possible problems ... NOTE
Dim: no visible global function definition for ‘is’
display.var: no visible global function definition for ‘is’
has.method: no visible global function definition for ‘showMethods’
headl: no visible global function definition for ‘is’
prv: no visible global function definition for ‘is’
summarise.r.datasets: no visible global function definition for ‘is’
Undefined global functions or variables:
is showMethods
Consider adding
importFrom("methods", "is", "showMethods")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘reader’
Maintainer: Dennis M. Feehan feehan@berkeley.edu
0 errors | 0 warnings | 0 notes
Maintainer: Devin Caughey devin.caughey@gmail.com
0 errors | 0 warnings | 0 notes
Maintainer: Di Cook dicook@iastate.edu
0 errors | 0 warnings | 1 note
checking R code for possible problems ... NOTE
box_dist: no visible global function definition for ‘quantile’
calc_mean_dist: no visible global function definition for ‘filter’
n: no visible global function definition for ‘resid’
null_dist : <anonymous>: no visible global function definition for
‘coef’
null_lm : <anonymous>: no visible global function definition for
‘predict’
reg_dist: no visible global function definition for ‘coef’
reg_dist: no visible global function definition for ‘lm’
... 10 lines ...
sep_dist: no visible global function definition for ‘cutree’
sep_dist: no visible global function definition for ‘hclust’
uni_dist: no visible global function definition for ‘sd’
Undefined global functions or variables:
coef cutree dist filter hclust lm predict quantile rbinom resid rnorm
sd update
Consider adding
importFrom("stats", "coef", "cutree", "dist", "filter", "hclust", "lm",
"predict", "quantile", "rbinom", "resid", "rnorm", "sd",
"update")
to your NAMESPACE file.
Maintainer: Hadley Wickham hadley@rstudio.com Bug reports: https://github.com/hadley/nycflights13/issues
0 errors | 0 warnings | 1 note
checking installed package size ... NOTE
installed size is 7.0Mb
sub-directories of 1Mb or more:
data 6.9Mb
Maintainer: David Carslaw david.carslaw@york.ac.uk Bug reports: https://github.com/davidcarslaw/openair/issues
0 errors | 0 warnings | 0 notes
Maintainer: Maëlle Salmon maelle.salmon@yahoo.se Bug reports: http://github.com/ropenscilabs/opencage/issues
0 errors | 0 warnings | 0 notes
Maintainer: Dangna Li ldangna@gmail.com
0 errors | 0 warnings | 1 note
checking R code for possible problems ... NOTE
PAC : clusterDist: no visible global function definition for ‘var’
PAC: no visible global function definition for ‘complete.cases’
Undefined global functions or variables:
complete.cases var
Consider adding
importFrom("stats", "complete.cases", "var")
to your NAMESPACE file.
Maintainer: Jirka Lewandowski jirka.lewandowski@wzb.eu Bug reports: http://gitlab.points-of-interest.cc/points-of-interest/packagetrackr/issues
0 errors | 0 warnings | 0 notes
Maintainer: Eric Hare erichare@iastate.edu Bug reports: https://github.com/heike/peptider/issues
0 errors | 0 warnings | 0 notes
Maintainer: Pedro J. Aphalo pedro.aphalo@helsinki.fi Bug reports: https://bitbucket.org/aphalo/photobiology/issues
1 error | 1 warning | 0 notes
checking examples ... ERROR
Running examples in ‘photobiology-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: absorbance
> ### Title: Absorbance
> ### Aliases: absorbance absorbance.default absorbance.filter_mspct
> ### absorbance.filter_spct absorbance.object_mspct absorbance.object_spct
>
> ### ** Examples
>
> absorbance(polyester.spct, new_waveband(400,700))
Error: evaluation nested too deeply: infinite recursion / options(expressions=)?
Execution halted
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
Error: processing vignette 'userguide.Rnw' failed with diagnostics:
evaluation nested too deeply: infinite recursion / options(expressions=)?
Execution halted
Maintainer: Pedro J. Aphalo pedro.aphalo@helsinki.fi Bug reports: https://bitbucket.org/aphalo/photobiologyinout/
0 errors | 1 warning | 0 notes
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
Read 3 items
Read 16 items
Error: processing vignette 'user-guide.Rnw' failed with diagnostics:
evaluation nested too deeply: infinite recursion / options(expressions=)?
Execution halted
Maintainer: Marco Blume marco.blume@pinnaclesports.com
0 errors | 0 warnings | 0 notes
Maintainer: Carson Sievert cpsievert1@gmail.com Bug reports: http://github.com/cpsievert/pitchRx/issues
0 errors | 0 warnings | 1 note
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘ggsubplot’
Maintainer: Benjamin Nutter nutter@battelle.org Bug reports: https://github.com/nutterb/pixiedust/issues
0 errors | 0 warnings | 0 notes
Maintainer: Scott Warchal s.warchal@sms.ed.ac.uk
0 errors | 0 warnings | 0 notes
Maintainer: Carson Sievert cpsievert1@gmail.com Bug reports: https://github.com/ropensci/plotly/issues
0 errors | 0 warnings | 0 notes
Maintainer: Carl Boettiger cboettig@gmail.com Bug reports: https://github.com/cboettig/pmc/issues
0 errors | 0 warnings | 0 notes
Maintainer: Przemyslaw Biecek przemyslaw.biecek@gmail.com
0 errors | 0 warnings | 1 note
checking installed package size ... NOTE
installed size is 6.1Mb
sub-directories of 1Mb or more:
data 6.0Mb
Maintainer: Jeffrey B. Arnold jeffrey.arnold@gmail.com Bug reports: https://github.com/rOpenGov/pollstR/issues
0 errors | 0 warnings | 0 notes
Maintainer: Andrew C. Hooker andrew.hooker@farmbio.uu.se Bug reports: https://github.com/andrewhooker/PopED/issues
0 errors | 0 warnings | 0 notes
Maintainer: Daniel Bottomly bottomly@ohsu.edu
0 errors | 1 warning | 2 notes
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
select
The following object is masked from ‘package:stats’:
filter
... 8 lines ...
Loading required package: DBI
Starting gender
Starting clinical
Starting samples
Starting dna
Error: processing vignette 'poplite.Rnw' failed with diagnostics:
chunk 15
Error in library(VariantAnnotation) :
there is no package called ‘VariantAnnotation’
Execution halted
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘VariantAnnotation’
checking R code for possible problems ... NOTE
filter_.Database: no visible global function definition for ‘stack’
get.starting.point : <anonymous>: no visible global function definition
for ‘na.omit’
select_.Database: no visible global function definition for ‘stack’
tsl.to.graph: no visible global function definition for ‘stack’
join,Database: no visible global function definition for ‘stack’
join,Database : .get.select.cols: no visible global function definition
for ‘setNames’
join,Database: no visible binding for global variable ‘new.ancil’
join,Database: no visible global function definition for ‘setNames’
Undefined global functions or variables:
na.omit new.ancil setNames stack
Consider adding
importFrom("stats", "na.omit", "setNames")
importFrom("utils", "stack")
to your NAMESPACE file.
Maintainer: Zhian N. Kamvar kamvarz@science.oregonstate.edu Bug reports: https://github.com/grunwaldlab/poppr/issues
0 errors | 0 warnings | 0 notes
Maintainer: Ayala S. Allon ayalaallon@gmail.com Bug reports: http://github.com/ayalaallon/prepdat/issues
0 errors | 0 warnings | 0 notes
Maintainer: Ankur Chakravarthy ankur.chakravarthy.10@ucl.ac.uk
1 error | 0 warnings | 0 notes
checking package dependencies ... ERROR
Package required but not available: ‘multtest’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Maintainer: Hadley Wickham hadley@rstudio.com Bug reports: https://github.com/hadley/purrr/issues
0 errors | 0 warnings | 0 notes
Maintainer: Tyler Rinker tyler.rinker@gmail.com Bug reports: http://github.com/trinker/qdap/issues
0 errors | 0 warnings | 0 notes
Maintainer: Michael D. Sumner mdsumner@gmail.com
0 errors | 0 warnings | 0 notes
Maintainer: Joel Gombin joel.gombin@gmail.com
0 errors | 0 warnings | 0 notes
Maintainer: Linares Daniel danilinares@gmail.com
0 errors | 0 warnings | 0 notes
Maintainer: Peter DeWitt dewittpe@gmail.com
0 errors | 0 warnings | 0 notes
Maintainer: Kristian D. Olsen kristian@doingit.no
0 errors | 0 warnings | 0 notes
Maintainer: Alexander Coppock ac3242@columbia.edu
0 errors | 0 warnings | 0 notes
Maintainer: Graham Williams Graham.Williams@togaware.com
0 errors | 0 warnings | 3 notes
checking package dependencies ... NOTE
Packages suggested but not available for checking:
‘graph’ ‘RBGL’ ‘rggobi’ ‘RODBC’ ‘pkgDepTools’ ‘Rgraphviz’
checking installed package size ... NOTE
installed size is 6.8Mb
sub-directories of 1Mb or more:
data 2.5Mb
etc 1.9Mb
po 1.2Mb
checking dependencies in R code ... NOTE
(R:75948): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
Maintainer: Scott Chamberlain myrmecocystus@gmail.com Bug reports: https://github.com/ropensci/rbison/issues
0 errors | 0 warnings | 0 notes
Maintainer: Erik Bulow erik.bulow@rccvast.se Bug reports: https://bitbucket.com/cancercentrum/rccmisc/issues
0 errors | 0 warnings | 0 notes
Maintainer: Joshua Kunst jbkunst@gmail.com Bug reports: https://github.com/jbkunst/rchess/issues
0 errors | 0 warnings | 0 notes
Maintainer: Ron Dotsch rdotsch@gmail.com
0 errors | 0 warnings | 0 notes
Maintainer: Kathe Todd-Brown ktoddbrown@gmail.com
1 error | 0 warnings | 3 notes
checking tests ... ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
1. Failure: makeGlobalStat sorts before computing (@test_makeGlobalStat.R#136) -
res1$val$value not equal to ans$value.
2/2 mismatches (average diff: 0.333)
[1] 1.17 - 1.5 == -0.333
[2] 1.17 - 1.5 == -0.333
testthat results ================================================================
OK: 422 SKIPPED: 20 FAILED: 1
1. Failure: makeGlobalStat sorts before computing (@test_makeGlobalStat.R#136)
Error: testthat unit tests failed
Execution halted
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘ncdf’
checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
‘ggplot2’ ‘ncdf’ ‘ncdf4’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
checking R code for possible problems ... NOTE
addProvenance: no visible global function definition for
‘packageVersion’
addProvenance: no visible global function definition for
‘capture.output’
cmip5data: no visible global function definition for ‘runif’
filterDimensionTimeMonths: no visible binding for global variable
‘time’
makeGlobalStat: no visible binding for global variable ‘weighted.mean’
makePackageData: no visible global function definition for
... 7 lines ...
worldPlot: no visible global function definition for ‘quantile’
worldPlot: no visible global function definition for ‘rainbow’
Undefined global functions or variables:
capture.output object.size packageVersion quantile rainbow runif time
weighted.mean write.csv
Consider adding
importFrom("grDevices", "rainbow")
importFrom("stats", "quantile", "runif", "time", "weighted.mean")
importFrom("utils", "capture.output", "object.size", "packageVersion",
"write.csv")
to your NAMESPACE file.
Maintainer: Scott Chamberlain myrmecocystus@gmail.com Bug reports: https://github.com/ropensci/rcrossref/issues
0 errors | 0 warnings | 0 notes
Maintainer: Konstantin A. Blagodatskikh k.blag@yandex.ru
0 errors | 0 warnings | 0 notes
Maintainer: Karthik Ram karthik.ram@gmail.com Bug reports: https://github.com/karthik/rdrop2/issues
0 errors | 0 warnings | 0 notes
Maintainer: Chung-hong Chan chainsawtiney@gmail.com
0 errors | 0 warnings | 0 notes
Maintainer: Sebastian Pardo sebpardo@gmail.com Bug reports: http://github.com/ropensci/rebird/issues
0 errors | 0 warnings | 0 notes
Maintainer: Julia Wrobel jw3134@cumc.columbia.edu
0 errors | 0 warnings | 0 notes
Maintainer: Scott Chamberlain myrmecocystus@gmail.com Bug reports: http://www.github.com/ropensci/rerddap/issues
0 errors | 0 warnings | 0 notes
Maintainer: Jared Lander packages@jaredlander.com Bug reports: https://github.com/jaredlander/resumer/issues
1 error | 0 warnings | 0 notes
checking tests ... ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
2. Failure: resumer returns an rmakdown object with the correct length and names (@test-resumerStructure.R#9)
names(resBlank) not equal to c(...).
Lengths differ: 9 vs 7
testthat results ================================================================
OK: 37 SKIPPED: 0 FAILED: 2
1. Failure: resumer returns an rmakdown object with the correct length and names (@test-resumerStructure.R#6)
2. Failure: resumer returns an rmakdown object with the correct length and names (@test-resumerStructure.R#9)
Error: testthat unit tests failed
Execution halted
Maintainer: Michael C Koohafkan michael.koohafkan@gmail.com Bug reports: https://github.com/mkoohafkan/reval/issues
0 errors | 0 warnings | 0 notes
Maintainer: Jim Hester james.f.hester@gmail.com Bug reports: https://github.com/kevinushey/rex/issues
0 errors | 0 warnings | 0 notes
Maintainer: Carl Boettiger cboettig@ropensci.org Bug reports: https://github.com/ropensci/rfishbase/issues
0 errors | 0 warnings | 0 notes
Maintainer: Antoine Filipovic-Pierucci pierucci@gmail.com Bug reports: https://github.com/pierucci/rgho/issues
0 errors | 0 warnings | 0 notes
Maintainer: Maëlle Salmon maelle.salmon@yahoo.se Bug reports: http://github.com/ropenscilabs/riem/issues
0 errors | 0 warnings | 1 note
checking DESCRIPTION meta-information ... NOTE
Authors@R field gives persons with no valid roles:
Brooke Anderson [rev] (Brooke Anderson reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/39.)
Maintainer: Michael C Koohafkan michael.koohafkan@gmail.com Bug reports: https://github.com/mkoohafkan/rivr/issues
0 errors | 0 warnings | 0 notes
Maintainer: Albertus J. Smit albertus.smit@gmail.com
0 errors | 0 warnings | 0 notes
Maintainer: Michal Draminski mdramins@ipipan.waw.pl
0 errors | 0 warnings | 0 notes
Maintainer: Carl Boettiger cboettig@gmail.com Bug reports: https://github.com/ropensci/RNeXML/issues
2 errors | 1 warning | 1 note
checking examples ... ERROR
Running examples in ‘RNeXML-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add_basic_meta
> ### Title: Add basic metadata
> ### Aliases: add_basic_meta
>
> ### ** Examples
>
> nex <- add_basic_meta(title = "My test title",
+ description = "A description of my test",
+ creator = "Carl Boettiger <cboettig@gmail.com>",
+ publisher = "unpublished data",
+ pubdate = "2012-04-01")
Error: Unknown column 'content'
Execution halted
checking tests ... ERROR
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
1. Error: We can serialize the various versions of the ape format (@test_ape.R#40)
2. Error: We can read and write NeXML to phylo and back without edge.lengths (@test_ape.R#52)
3. Error: Rooted trees remain rooted on conversions (@test_ape.R#65)
4. Error: Unrooted trees remain unrooted on conversions (@test_ape.R#74)
5. Error: we can extract character matrix with get_characters (@test_characters.R#44)
6. Error: we can add characters to a nexml file using a data.frame (@test_characters.R#88)
7. Error: We can extract tree and trait data to run fitContinuous and fitDiscrete (@test_comp_analysis.R#9)
8. Error: We can serialize tree and trait data for a comparative analysis (@test_comp_analysis.R#25)
9. Error: Getting characters (@test_get_characters.R#7)
1. ...
Error: testthat unit tests failed
Execution halted
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
Loading required package: ape
Quitting from lines 46-67 (metadata.Rmd)
Error: processing vignette 'metadata.Rmd' failed with diagnostics:
Unknown column 'content'
Execution halted
checking package dependencies ... NOTE
Packages suggested but not available for checking: ‘rrdf’ ‘Sxslt’
Maintainer: Scott Chamberlain myrmecocystus@gmail.com Bug reports: http://www.github.com/ropensci/rnoaa/issues
0 errors | 0 warnings | 0 notes
Maintainer: Peter Meissner retep.meissner@gmail.com Bug reports: https://github.com/ropenscilabs/robotstxt/issues
0 errors | 0 warnings | 0 notes
Maintainer: Ruokun Huang hruokun.2008@gmail.com
0 errors | 0 warnings | 0 notes
Maintainer: David Springate daspringate@gmail.com
0 errors | 0 warnings | 0 notes
Maintainer: Joe Thorley joe@poissonconsulting.ca
0 errors | 0 warnings | 0 notes
Maintainer: Enzo Martoglio enzo@smartinsightsfromdata.com
0 errors | 0 warnings | 0 notes
Maintainer: Eduardo Ibanez edu.ibanez@gmail.com Bug reports: https://github.com/NREL/rplexos/issues
1 error | 1 warning | 0 notes
checking examples ... ERROR
Running examples in ‘rplexos-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: process_folder
> ### Title: Convert PLEXOS files to SQLite databases
> ### Aliases: process_folder process_input process_solution
>
> ### ** Examples
>
> # Process the folder with the solution file provided by rplexos
> location <- location_solution_rplexos()
> process_folder(location)
Warning: `rbind_list()` is deprecated. Please use `bind_rows()` instead.
>
> # Process the folder with the input file provided by rplexos
> location2 <- location_input_rplexos()
> process_folder(location2)
Error in sqliteSendQuery(con, statement, bind.data) :
error in statement: no such column: comp_collection
Calls: process_folder ... .local -> sqliteGetQuery -> sqliteSendQuery -> .Call
Execution halted
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
Quitting from lines 186-187 (rplexos.Rmd)
Error: processing vignette 'rplexos.Rmd' failed with diagnostics:
error in statement: no such column: comp_collection
Execution halted
Maintainer: Scott Chamberlain myrmecocystus@gmail.com Bug reports: https://github.com/ropensci/rplos/issues
0 errors | 0 warnings | 0 notes
Maintainer: Patrick Roocks mail@p-roocks.de
0 errors | 0 warnings | 1 note
checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
Maintainer: Onur Ismail Filiz onur@fb.com Bug reports: https://github.com/prestodb/RPresto/issues
0 errors | 0 warnings | 0 notes
Maintainer: Stuart Lacy stuart.lacy@york.ac.uk
0 errors | 0 warnings | 0 notes
Maintainer: Benjamin Skinner b.skinner@vanderbilt.edu Bug reports: http://github.com/btskinner/rscorecard/issues
0 errors | 0 warnings | 0 notes
Maintainer: Imanuel Costigan i.costigan@me.com Bug reports: https://github.com/imanuelcostigan/RSQLServer/issues
1 error | 0 warnings | 0 notes
checking whether package ‘RSQLServer’ can be installed ... ERROR
Installation failed.
See ‘/Users/hadley/Documents/dplyr/dplyr/revdep/checks/RSQLServer.Rcheck/00install.out’ for details.
Maintainer: David Gohel david.gohel@lysis-consultants.fr Bug reports: https://github.com/davidgohel/rtable/issues
0 errors | 0 warnings | 0 notes
Maintainer: Henrik Singmann singmann+rtdists@gmail.com
0 errors | 0 warnings | 0 notes
Maintainer: Scott Chamberlain myrmecocystus@gmail.com Bug reports: https://github.com/ropengov/rtimes/issues
0 errors | 0 warnings | 0 notes
Maintainer: Anup Nair nairanup50695@gmail.com
0 errors | 0 warnings | 0 notes
Maintainer: Scott Chamberlain myrmecocystus@gmail.com Bug reports: https://github.com/ropensci/rvertnet/issues
0 errors | 0 warnings | 0 notes
Maintainer: Alex Shum alex@ALShum.com Bug reports: https://github.com/alshum/rwunderground/issues
0 errors | 0 warnings | 0 notes
Maintainer: Sebastian Warnholz Sebastian.Warnholz@fu-berlin.de Bug reports: https://github.com/wahani/saeSim/issues
0 errors | 0 warnings | 0 notes
Maintainer: James Keirstead james.keirstead@gmail.com Bug reports: https://github.com/jkeirstead/scholar/issues
0 errors | 0 warnings | 0 notes
Maintainer: Tomas Radivoyevitch radivot@ccf.org
0 errors | 0 warnings | 0 notes
Maintainer: Piotr Smuda piotrsmuda@gmail.com Bug reports: http://github.com/mi2-warsaw/sejmRP/issues
0 errors | 0 warnings | 0 notes
Maintainer: Jason Vander Heiden jason.vanderheiden@yale.edu Bug reports: https://bitbucket.org/kleinstein/shazam/issues
0 errors | 0 warnings | 0 notes
Maintainer: Jeff Allen cran@trestletechnology.net Bug reports: https://github.com/trestletech/shinyAce/issues
0 errors | 0 warnings | 1 note
checking installed package size ... NOTE
installed size is 9.9Mb
sub-directories of 1Mb or more:
www 9.7Mb
Maintainer: Phil Chalmers rphilip.chalmers@gmail.com
0 errors | 0 warnings | 1 note
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘doMPI’
Maintainer: Iñaki Ucar i.ucar86@gmail.com Bug reports: https://github.com/Enchufa2/simmer/issues
0 errors | 0 warnings | 0 notes
Maintainer: Christopher Gandrud christopher.gandrud@gmail.com Bug reports: https://github.com/christophergandrud/simPH/issues
0 errors | 0 warnings | 0 notes
Maintainer: Daniel Lüdecke d.luedecke@uke.de
0 errors | 0 warnings | 0 notes
Maintainer: Daniel Lüdecke d.luedecke@uke.de Bug reports: https://github.com/sjPlot/devel/issues
0 errors | 0 warnings | 0 notes
Maintainer: Bob Rudis bob@rudis.net Bug reports: https://github.com/hrbrmstr/slackr/issues
0 errors | 0 warnings | 0 notes
Maintainer: Scott Chamberlain myrmecocystus@gmail.com Bug reports: http://www.github.com/ropensci/solrium/issues
0 errors | 0 warnings | 0 notes
Maintainer: Leo Lahti louhos@googlegroups.com Bug reports: https://github.com/ropengov/sorvi/issues
0 errors | 0 warnings | 1 note
checking R code for possible problems ... NOTE
convert_municipality_names: no visible global function definition for
‘read.csv’
regression_plot: no visible binding for global variable ‘loess’
regression_plot: no visible global function definition for
‘colorRampPalette’
regression_plot: no visible global function definition for
‘loess.control’
regression_plot: no visible global function definition for ‘predict’
regression_plot : <anonymous>: no visible global function definition
for ‘quantile’
regression_plot : <anonymous>: no visible global function definition
for ‘pnorm’
regression_plot: no visible global function definition for
‘flush.console’
regression_plot: no visible global function definition for ‘density’
Undefined global functions or variables:
colorRampPalette density flush.console loess loess.control pnorm
predict quantile read.csv
Consider adding
importFrom("grDevices", "colorRampPalette")
importFrom("stats", "density", "loess", "loess.control", "pnorm",
"predict", "quantile")
importFrom("utils", "flush.console", "read.csv")
to your NAMESPACE file.
Maintainer: George Fisher george@georgefisher.com
0 errors | 0 warnings | 0 notes
Maintainer: Alex M Chubaty alexander.chubaty@canada.ca Bug reports: https://github.com/PredictiveEcology/SpaDES/issues
0 errors | 1 warning | 1 note
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
Loading required package: grid
Attaching package: 'grid'
The following object is masked from 'package:SpaDES':
... 8 lines ...
shift
The following object is masked from 'package:SpaDES':
copy
Files saved. Use outputs(your simList) for details
Quitting from lines 581-622 (ii-modules.Rmd)
Error: processing vignette 'ii-modules.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
Execution halted
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘fastshp’
Maintainer: Michael D. Sumner mdsumner@gmail.com
0 errors | 0 warnings | 0 notes
Maintainer: Brandon Taylor brandon.taylor221@gmail.com Bug reports: https://github.com/bramtayl/sprintfr/issues
1 error | 1 warning | 0 notes
checking examples ... ERROR
Running examples in ‘sprintfr-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: string_base
> ### Title: Get a list of base string components for building string formats
> ### Aliases: string_base
> ### Keywords: datasets
>
> ### ** Examples
>
> string_base
integer octal hex double scientific auto binary string percent
1 i o x f e g a s %
> string_format(integer, " ", double)
Error: object 'data_frame' not found
Execution halted
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
Quitting from lines 30-31 (sprintfr.Rmd)
Error: processing vignette 'sprintfr.Rmd' failed with diagnostics:
object 'data_frame' not found
Execution halted
Maintainer: Greg Freedman greg.freedman@gmail.com Bug reports: https://github.com/gergness/srvyr/issues
0 errors | 0 warnings | 0 notes
Maintainer: Sean Anderson sean@seananderson.ca
0 errors | 0 warnings | 0 notes
Maintainer: Matthieu Gomez mattg@princeton.edu Bug reports: https://github.com/matthieugomez/statar/issues
1 error | 0 warnings | 1 note
checking examples ... ERROR
Running examples in ‘statar-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: find_duplicates
> ### Title: returns a data.frame with duplicated rows
> ### Aliases: find_duplicates find_duplicates_
>
> ### ** Examples
>
> df <- data.frame(a = rep(1:2, each = 3), b = 1:6)
> find_duplicates(df, a)
2 groups have duplicates
Error in eval(expr, envir, enclos) : could not find function "everything"
Calls: find_duplicates ... select_vars_ -> <Anonymous> -> lapply -> FUN -> eval -> eval
Execution halted
checking dependencies in R code ... NOTE
Missing or unexported object: ‘dplyr::tbl_dt’
Maintainer: Richard Iannone riannone@me.com Bug reports: https://github.com/rich-iannone/stationaRy/issues
0 errors | 0 warnings | 1 note
checking installed package size ... NOTE
installed size is 8.1Mb
Maintainer: Robin Lovelace rob00x@gmail.com Bug reports: https://github.com/ropensci/stplanr/issues
0 errors | 0 warnings | 0 notes
Maintainer: Brandon Taylor brandon.taylor221@gmail.com
0 errors | 0 warnings | 0 notes
Maintainer: Dennis M. Feehan feehan@berkeley.edu
0 errors | 0 warnings | 0 notes
Maintainer: Marcus W. Beck mbafs2012@gmail.com Bug reports: https://github.com/fawda123/SWMPr/issues
0 errors | 0 warnings | 0 notes
Maintainer: Seth Wenchel seth@wenchel.com Bug reports: http://github.com/restonslacker/taber/issues
0 errors | 0 warnings | 0 notes
Maintainer: Lukas Burk lukas@quantenbrot.de Bug reports: https://github.com/tadaadata/tadaatoolbox/issues
0 errors | 0 warnings | 0 notes
Maintainer: Vadim Nazarov vdm.nazarov@gmail.com Bug reports: https://github.com/imminfo/tcr/issues
0 errors | 0 warnings | 1 note
checking installed package size ... NOTE
installed size is 5.6Mb
sub-directories of 1Mb or more:
data 1.2Mb
doc 3.9Mb
Maintainer: George Wang biogeek@gmail.com
0 errors | 0 warnings | 1 note
checking installed package size ... NOTE
installed size is 5.9Mb
sub-directories of 1Mb or more:
data 5.9Mb
Maintainer: Scott Olesen swo@mit.edu
0 errors | 1 warning | 0 notes
checking whether package ‘texmexseq’ can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘dplyr::matches’ by ‘testthat::matches’ when loading ‘texmexseq’
See ‘/Users/hadley/Documents/dplyr/dplyr/revdep/checks/texmexseq.Rcheck/00install.out’ for details.
Maintainer: Lincoln Mullen lincoln@lincolnmullen.com Bug reports: https://github.com/ropensci/textreuse/issues
0 errors | 0 warnings | 0 notes
Maintainer: Torsten Hothorn Torsten.Hothorn@R-project.org
0 errors | 0 warnings | 1 note
checking installed package size ... NOTE
installed size is 5.2Mb
sub-directories of 1Mb or more:
data 1.1Mb
rda 3.8Mb
Maintainer: Jeremy Stanley jeremy.stanley@gmail.com
0 errors | 0 warnings | 1 note
checking R code for possible problems ... NOTE
read_json: no visible global function definition for ‘tail’
Undefined global functions or variables:
tail
Consider adding
importFrom("utils", "tail")
to your NAMESPACE file.
Maintainer: Hadley Wickham hadley@rstudio.com Bug reports: https://github.com/hadley/tidyr/issues
0 errors | 0 warnings | 0 notes
Maintainer: Julia Silge julia.silge@gmail.com Bug reports: http://github.com/juliasilge/tidytext/issues
2 errors | 1 warning | 0 notes
checking examples ... ERROR
Running examples in ‘tidytext-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cast_sparse
> ### Title: Create a sparse matrix from row names, column names, and values
> ### in a table.
> ### Aliases: cast_sparse
>
... 7 lines ...
>
> cast_sparse(dat, a, b)
2 x 4 sparse Matrix of class "dgCMatrix"
col1 col2 col3 col4
row1 1 1 . .
row2 1 . 1 1
>
> cast_sparse(dat, a, b, val)
Error in .M.kind(x) : not yet implemented for matrix with typeof NULL
Calls: cast_sparse -> cast_sparse_ -> <Anonymous> -> .M.kind
Execution halted
checking tests ... ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
1: cast_sparse(dat, a, b, val) at testthat/test-sparse-casters.R:20
2: cast_sparse_(data, col_name(substitute(row)), col_name(substitute(column)), value_col)
3: data[[value_col]]
4: `[[.tbl_df`(data, value_col)
5: stopc("Unknown column '", colname, "'") at /private/tmp/RtmpxqBRhg/devtools1785e2d679c7f/hadley-tibble-1e5b140/R/tbl-df.r:25
6: stop(..., call. = FALSE, domain = NA) at /private/tmp/RtmpxqBRhg/devtools1785e2d679c7f/hadley-tibble-1e5b140/R/utils.r:63
testthat results ================================================================
OK: 41 SKIPPED: 0 FAILED: 1
1. Error: Can cast tables into a sparse Matrix (@test-sparse-casters.R#20)
Error: testthat unit tests failed
Execution halted
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
Warning: Stacking not well defined when ymin != 0
Quitting from lines 94-114 (tidying_casting.Rmd)
Error: processing vignette 'tidying_casting.Rmd' failed with diagnostics:
Unknown column 'count'
Execution halted
Maintainer: Daniel Gadala-Maria daniel.gadala-maria@yale.edu Bug reports: https://bitbucket.org/kleinstein/tigger/issues
1 error | 1 warning | 0 notes
checking examples ... ERROR
Running examples in ‘tigger-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getPopularMutationCount
> ### Title: Find Frequent Sequences' Mutation Counts
> ### Aliases: getPopularMutationCount
>
> ### ** Examples
>
> data(sample_db, germline_ighv)
> getPopularMutationCount(sample_db, germline_ighv)
Error: object 'V_GENE_N' not found
Execution halted
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
Loading required package: alakazam
Loading required package: ggplot2
Loading required package: shazam
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
Quitting from lines 110-115 (Tigger-Vignette.Rmd)
Error: processing vignette 'Tigger-Vignette.Rmd' failed with diagnostics:
there is no package called 'snow'
Execution halted
Maintainer: Kyle Walker kyle.walker@tcu.edu
0 errors | 0 warnings | 0 notes
Maintainer: Paul Hendricks paul.hendricks.2013@owu.edu Bug reports: https://github.com/paulhendricks/titanic/issues
0 errors | 0 warnings | 0 notes
Maintainer: Stephen Turner vustephen@gmail.com
0 errors | 0 warnings | 0 notes
Maintainer: Scott Chamberlain myrmecocystus@gmail.com Bug reports: http://www.github.com/ropensci/traits/issues
0 errors | 0 warnings | 0 notes
Maintainer: Josef Uyeda josef.uyeda@gmail.com
0 errors | 1 warning | 0 notes
checking examples ... WARNING
Found the following significant warnings:
Warning: Setting row names on a tibble is deprecated.
Warning: Setting row names on a tibble is deprecated.
Warning: Setting row names on a tibble is deprecated.
Warning: Setting row names on a tibble is deprecated.
Warning: Setting row names on a tibble is deprecated.
Warning: Setting row names on a tibble is deprecated.
Warning: Setting row names on a tibble is deprecated.
Warning: Setting row names on a tibble is deprecated.
Warning: Setting row names on a tibble is deprecated.
Warning: Setting row names on a tibble is deprecated.
Warning: Setting row names on a tibble is deprecated.
Warning: Setting row names on a tibble is deprecated.
Warning: Setting row names on a tibble is deprecated.
Warning: Setting row names on a tibble is deprecated.
Warning: Setting row names on a tibble is deprecated.
Warning: Setting row names on a tibble is deprecated.
Warning: Setting row names on a tibble is deprecated.
Warning: Setting row names on a tibble is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Maintainer: Ryan Hafen rhafen@gmail.com Bug reports: https://github.com/tesseradata/trelliscope/issues
0 errors | 0 warnings | 0 notes
Maintainer: Jack Horne jack@jackhorne.net
0 errors | 0 warnings | 1 note
checking R code for possible problems ... NOTE
turf: no visible global function definition for ‘read.table’
turf: no visible global function definition for ‘flush.console’
turf.combos: no visible global function definition for ‘combn’
Undefined global functions or variables:
combn flush.console read.table
Consider adding
importFrom("utils", "combn", "flush.console", "read.table")
to your NAMESPACE file.
Maintainer: Jared P. Lander packages@jaredlander.com
1 error | 0 warnings | 0 notes
checking tests ... ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
4. Failure: simple.impute.default properly imputes the mean (@test-simple-impute.r#41)
all.equal(...) produced no output
testthat results ================================================================
OK: 324 SKIPPED: 0 FAILED: 4
1. Failure: simple.impute.default properly imputes the mean (@test-simple-impute.r#32)
2. Failure: simple.impute.default properly imputes the mean (@test-simple-impute.r#35)
3. Failure: simple.impute.default properly imputes the mean (@test-simple-impute.r#38)
4. Failure: simple.impute.default properly imputes the mean (@test-simple-impute.r#41)
Error: testthat unit tests failed
Execution halted
Maintainer: Irucka Embry iembry@ecoccs.com Bug reports: https://gitlab.com/iembry/vaersND/issues
0 errors | 0 warnings | 0 notes
Maintainer: Irucka Embry iembry@ecoccs.com Bug reports: https://gitlab.com/iembry/vaers/issues
0 errors | 0 warnings | 0 notes
Maintainer: Brian J. Knaus briank.lists@gmail.com
1 error | 0 warnings | 0 notes
checking examples ... ERROR
Running examples in ‘vcfR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Convert to tidy data frames
> ### Title: Convert vcfR objects to tidy data frames
> ### Aliases: 'Convert to tidy data frames' extract_gt_tidy
> ### extract_info_tidy vcfR2tidy vcf_field_names
>
... 8 lines ...
> # data frames: fix, gt, and meta. Here we don't coerce columns
> # to integer or numeric types...
> Z <- vcfR2tidy(vcf)
Extracting gt element AD
Extracting gt element DP
Extracting gt element GQ
Extracting gt element GT
Extracting gt element PL
Error in eval(expr, envir, enclos) : could not find function "everything"
Calls: vcfR2tidy ... select_vars_ -> <Anonymous> -> lapply -> FUN -> eval -> eval
Execution halted
Maintainer: Tomokazu Fujino fujino@fwu.ac.jp
0 errors | 0 warnings | 0 notes
Maintainer: Robert Corty rcorty@gmail.com
0 errors | 0 warnings | 0 notes
Maintainer: John Mount jmount@win-vector.com
0 errors | 0 warnings | 0 notes
Maintainer: Vincent Porretta vincentporretta@gmail.com
0 errors | 0 warnings | 0 notes
Maintainer: Tyler Rinker tyler.rinker@gmail.com Bug reports: https://github.com/trinker/wakefield/issues
0 errors | 0 warnings | 0 notes
Maintainer: Eric Persson expersso5@gmail.com Bug reports: https://www.github.com/expersso/WHO/issues
0 errors | 0 warnings | 0 notes
Maintainer: Peter Meissner retep.meissner@gmail.com Bug reports: https://github.com/petermeissner/wikipediatrend/issues
0 errors | 0 warnings | 1 note
checking package dependencies ... NOTE
Packages suggested but not available for checking:
‘AnomalyDetection’ ‘BreakoutDetection’
Maintainer: Mika Braginsky mika.br@gmail.com Bug reports: http://github.com/langcog/wordbankr/issues
0 errors | 0 warnings | 0 notes
Maintainer: Kirill Müller krlmlr+r@mailbox.org Bug reports: https://github.com/krlmlr/wrswoR.benchmark/issues
0 errors | 0 warnings | 0 notes
Maintainer: Kirill Müller krlmlr+r@mailbox.org Bug reports: https://github.com/krlmlr/wrswoR/issues
0 errors | 0 warnings | 0 notes
Maintainer: John Malc cincenko@outlook.com Bug reports: http://github.com/dmpe/wufoor/issues
0 errors | 0 warnings | 0 notes
Maintainer: Tinniam V Ganesh tvganesh.85@gmail.com
0 errors | 0 warnings | 0 notes
Maintainer: James Honaker zelig-zee@iq.harvard.edu
0 errors | 0 warnings | 0 notes
Maintainer: James Honaker zelig-zee@iq.harvard.edu
0 errors | 0 warnings | 0 notes
Maintainer: James Honaker zelig.zee@gmail.com
0 errors | 0 warnings | 0 notes
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