revdep check for CRAN submission

wilkelab · Dec 17, 2017 · 86d5c3f · 86d5c3f
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diff --git a/cran-comments.md b/cran-comments.md
@@ -1,25 +1,12 @@
-The package version I submitted yesterday did not build successfully when the magick package wasn't installed: https://cran.r-project.org/web/checks/check_results_cowplot.html This submission fixes that issue.
-
-I have also fixed the problem (noted yesterday) of examples that take longer than 10s to run. No other changes were made.
+This is a minor bugfix release that closes bugs related to plots showing up in the wrong places
+in shiny apps and extra blank plots popping up in knitted documents.
 
 ## Test environments
 * R devel on win-builder [ via devtools::build_win() ]
 * local OS X install x86_64-apple-darwin15.6.0 (64-bit), R 3.4.2
 
 ## R CMD check results
-There were no ERRORs or WARNINGs.
-
-There was one NOTE:
-Days since last update: 0
-
-I'm resubmitting so quickly because I received a request to do so by Brian Ripley:
-
-"You have added Suggests: magick but not used it conditionally as required in §1.1.3.1 of the manual.
-
-ImageMagick is a large install; moreover the C++ interface which 'magick' unnecessarily requires is not normally installed.
-
-Please correct ASAP once all the results are in."
-
+There were no ERRORs, WARNINGs, or NOTEs.
 
 ## Downstream dependencies
 Seem fine, according to devtools::revdep_check().
@@ -28,28 +15,28 @@ not because of cowplot.
 
 Full results available at https://github.com/wilkelab/cowplot/blob/master/revdep/README.md
 
-21 packages
-
 |package      |version | errors| warnings| notes|
 |:------------|:-------|------:|--------:|-----:|
-|bigstatsr    |0.2.2   |      1|        0|     0|
+|bigstatsr    |0.2.3   |      1|        0|     0|
 |deconvolveR  |1.0-3   |      0|        0|     0|
 |DGCA         |1.0.1   |      1|        0|     0|
+|ESTER        |0.2.0   |      0|        0|     0|
 |ggpubr       |0.1.6   |      0|        0|     1|
 |IncucyteDRC  |0.5.4   |      0|        0|     0|
 |jtools       |0.9.0   |      0|        0|     1|
-|JWileymisc   |0.2.1   |      0|        0|     0|
-|meme         |0.0.7   |      0|        0|     0|
+|JWileymisc   |0.2.1   |      0|        1|     0|
+|meme         |0.1.1   |      0|        1|     1|
 |memery       |0.3.1   |      0|        0|     0|
 |modcmfitr    |0.1.0   |      0|        0|     0|
-|oddsratio    |1.0.0   |      0|        0|     0|
-|pcr          |1.0.1   |      0|        0|     0|
+|oddsratio    |1.0.2   |      0|        0|     0|
+|pcr          |1.1.0   |      0|        1|     0|
 |poppr        |2.5.0   |      1|        0|     0|
 |preText      |0.6.1   |      0|        0|     0|
-|RNOmni       |0.1.3   |      0|        0|     0|
+|RNOmni       |0.1.4   |      0|        0|     0|
+|scatr        |1.0.1   |      0|        0|     0|
 |Seurat       |2.1.0   |      1|        0|     1|
 |sicegar      |0.2.2   |      0|        0|     0|
 |survivALL    |0.9.1   |      1|        0|     0|
-|tadaatoolbox |0.14.0  |      0|        0|     1|
+|tadaatoolbox |0.15.0  |      0|        0|     0|
 |valr         |0.3.1   |      0|        0|     1|
 |vanddraabe   |1.0.0   |      0|        0|     0|
diff --git a/revdep/README.md b/revdep/README.md
@@ -10,48 +10,58 @@
 |language |(EN)                         |
 |collate  |en_US.UTF-8                  |
 |tz       |America/Chicago              |
-|date     |2017-11-15                   |
+|date     |2017-12-16                   |
 
 ## Packages
 
-|package |*  |version |date       |source                      |
-|:-------|:--|:-------|:----------|:---------------------------|
-|covr    |   |3.0.1   |2017-11-07 |cran (@3.0.1)               |
-|cowplot |   |0.9.0   |2017-11-15 |local (wilkelab/cowplot@NA) |
-|dplyr   |*  |0.7.4   |2017-09-28 |cran (@0.7.4)               |
-|magick  |   |1.5     |2017-11-03 |cran (@1.5)                 |
-|tidyr   |*  |0.7.2   |2017-10-16 |cran (@0.7.2)               |
-|vdiffr  |   |0.2.1   |2017-10-09 |cran (@0.2.1)               |
+|package  |*  |version |date       |source                      |
+|:--------|:--|:-------|:----------|:---------------------------|
+|covr     |   |3.0.1   |2017-11-07 |cran (@3.0.1)               |
+|cowplot  |   |0.9.2   |2017-12-16 |local (wilkelab/cowplot@NA) |
+|dplyr    |   |0.7.4   |2017-09-28 |cran (@0.7.4)               |
+|ggplot2  |   |2.2.1   |2016-12-30 |cran (@2.2.1)               |
+|gtable   |   |0.2.0   |2016-02-26 |cran (@0.2.0)               |
+|knitr    |   |1.17    |2017-08-10 |cran (@1.17)                |
+|magick   |   |1.6     |2017-12-01 |cran (@1.6)                 |
+|maps     |   |3.2.0   |2017-06-08 |cran (@3.2.0)               |
+|plyr     |   |1.8.4   |2016-06-08 |cran (@1.8.4)               |
+|scales   |   |0.5.0   |2017-08-24 |cran (@0.5.0)               |
+|testthat |   |2.0.0   |2017-12-13 |cran (@2.0.0)               |
+|tidyr    |   |0.7.2   |2017-10-16 |cran (@0.7.2)               |
+|vdiffr   |   |0.2.1   |2017-10-09 |cran (@0.2.1)               |
+|viridis  |   |0.4.0   |2017-03-27 |cran (@0.4.0)               |
 
 # Check results
 
-21 packages
+23 packages
 
 |package      |version | errors| warnings| notes|
 |:------------|:-------|------:|--------:|-----:|
-|bigstatsr    |0.2.2   |      1|        0|     0|
+|bigstatsr    |0.2.3   |      1|        0|     0|
 |deconvolveR  |1.0-3   |      0|        0|     0|
 |DGCA         |1.0.1   |      1|        0|     0|
+|ESTER        |0.2.0   |      0|        0|     0|
 |ggpubr       |0.1.6   |      0|        0|     1|
 |IncucyteDRC  |0.5.4   |      0|        0|     0|
 |jtools       |0.9.0   |      0|        0|     1|
-|JWileymisc   |0.2.1   |      0|        0|     0|
-|meme         |0.0.7   |      0|        0|     0|
+|JWileymisc   |0.2.1   |      0|        1|     0|
+|meme         |0.1.1   |      0|        1|     1|
 |memery       |0.3.1   |      0|        0|     0|
 |modcmfitr    |0.1.0   |      0|        0|     0|
-|oddsratio    |1.0.0   |      0|        0|     0|
-|pcr          |1.0.1   |      0|        0|     0|
+|oddsratio    |1.0.2   |      0|        0|     0|
+|pcr          |1.1.0   |      0|        1|     0|
 |poppr        |2.5.0   |      1|        0|     0|
 |preText      |0.6.1   |      0|        0|     0|
-|RNOmni       |0.1.3   |      0|        0|     0|
+|RNOmni       |0.1.4   |      0|        0|     0|
+|scatr        |1.0.1   |      0|        0|     0|
 |Seurat       |2.1.0   |      1|        0|     1|
 |sicegar      |0.2.2   |      0|        0|     0|
 |survivALL    |0.9.1   |      1|        0|     0|
-|tadaatoolbox |0.14.0  |      0|        0|     1|
+|tadaatoolbox |0.15.0  |      0|        0|     0|
 |valr         |0.3.1   |      0|        0|     1|
 |vanddraabe   |1.0.0   |      0|        0|     0|
 
-## bigstatsr (0.2.2)
+## bigstatsr (0.2.3)
 Maintainer: Florian Privé <florian.prive.21@gmail.com>  
 Bug reports: https://github.com/privefl/bigstatsr/issues
 
@@ -76,7 +86,7 @@ Maintainer: Andrew McKenzie <amckenz@gmail.com>
 
 ```
 checking package dependencies ... ERROR
-Packages required but not available: ‘WGCNA’ ‘matrixStats’
+Package required but not available: ‘WGCNA’
 
 Packages suggested but not available for checking:
   ‘impute’ ‘fdrtool’ ‘GOstats’ ‘HGNChelper’ ‘org.Hs.eg.db’
@@ -86,6 +96,12 @@ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
 manual.
 ```
 
+## ESTER (0.2.0)
+Maintainer: Ladislas Nalborczyk <ladislas.nalborczyk@gmail.com>  
+Bug reports: https://github.com/lnalborczyk/ESTER/issues
+
+0 errors | 0 warnings | 0 notes
+
 ## ggpubr (0.1.6)
 Maintainer: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>  
 Bug reports: https://github.com/kassambara/ggpubr/issues
@@ -118,13 +134,36 @@ Packages unavailable to check Rd xrefs: ‘effects’, ‘ReporteRs’, ‘arm
 Maintainer: Joshua F. Wiley <jwiley.psych@gmail.com>  
 Bug reports: https://github.com/JWiley/JWileymisc/issues
 
-0 errors | 0 warnings | 0 notes
+0 errors | 1 warning  | 0 notes
+
+```
+checking whether package ‘JWileymisc’ can be installed ... WARNING
+Found the following significant warnings:
+  Warning: package ‘foreach’ was built under R version 3.4.3
+See ‘/Users/wilke/github/cowplot/revdep/checks/JWileymisc.Rcheck/00install.out’ for details.
+```
 
-## meme (0.0.7)
+## meme (0.1.1)
 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>  
 Bug reports: https://github.com/GuangchuangYu/meme/issues
 
-0 errors | 0 warnings | 0 notes
+0 errors | 1 warning  | 1 note 
+
+```
+checking re-building of vignette outputs ... WARNING
+Error in re-building vignettes:
+  ...
+Quitting from lines 167-177 (meme.Rmd) 
+Error: processing vignette 'meme.Rmd' failed with diagnostics:
+unused argument (data = d)
+Execution halted
+
+
+checking installed package size ... NOTE
+  installed size is  5.4Mb
+  sub-directories of 1Mb or more:
+    doc   4.9Mb
+```
 
 ## memery (0.3.1)
 Maintainer: Matthew Leonawicz <mfleonawicz@alaska.edu>  
@@ -137,17 +176,42 @@ Maintainer: Ed Wilson <ed.wilson@medschl.cam.ac.uk>
 
 0 errors | 0 warnings | 0 notes
 
-## oddsratio (1.0.0)
+## oddsratio (1.0.2)
 Maintainer: Patrick Schratz <patrick.schratz@gmail.com>  
 Bug reports: https://github.com/pat-s/oddsratio/issues
 
 0 errors | 0 warnings | 0 notes
 
-## pcr (1.0.1)
+## pcr (1.1.0)
 Maintainer: Mahmoud Ahmed <mahmoud.s.fahmy@students.kasralainy.edu.eg>  
 Bug reports: https://github.com/MahShaaban/pcr/issues
 
-0 errors | 0 warnings | 0 notes
+0 errors | 1 warning  | 0 notes
+
+```
+checking re-building of vignette outputs ... WARNING
+Error in re-building vignettes:
+  ...
+Joining, by = c("group", "gene")
+Joining, by = c("group", "gene")
+Joining, by = "gene"
+Joining, by = c("group", "gene")
+Joining, by = c("group", "gene")
+Parsed with column specification:
+cols(
+... 8 lines ...
+! LaTeX Error: \caption outside float.
+
+See the LaTeX manual or LaTeX Companion for explanation.
+Type  H <return>  for immediate help.
+ ...                                              
+                                                  
+l.528 \caption
+
+Error: processing vignette 'qpcr_analysis.Rmd' failed with diagnostics:
+pandoc document conversion failed with error 43
+Execution halted
+```
 
 ## poppr (2.5.0)
 Maintainer: Zhian N. Kamvar <zkamvar@gmail.com>  
@@ -166,11 +230,17 @@ Maintainer: Matthew J. Denny <mdenny@psu.edu>
 
 0 errors | 0 warnings | 0 notes
 
-## RNOmni (0.1.3)
+## RNOmni (0.1.4)
 Maintainer: Zachary McCaw <zmccaw@g.harvard.edu>
 
 0 errors | 0 warnings | 0 notes
 
+## scatr (1.0.1)
+Maintainer: Ravi Selker <selker.ravi@gmail.com>  
+Bug reports: https://github.com/raviselker/scatr/issues
+
+0 errors | 0 warnings | 0 notes
+
 ## Seurat (2.1.0)
 Maintainer: Paul Hoffman <seuratpackage@gmail.com>  
 Bug reports: https://github.com/satijalab/seurat/issues
@@ -201,24 +271,19 @@ Maintainer: Dominic Pearce <dominic.pearce@ed.ac.uk>
 ```
 checking package dependencies ... ERROR
 Packages required but not available:
-  ‘survcomp’ ‘survsim’ ‘Biobase’ ‘desiR’ ‘ggthemes’ ‘pander’
+  ‘survcomp’ ‘survsim’ ‘Biobase’ ‘desiR’ ‘pander’
 
 Package suggested but not available for checking: ‘GGally’
 
 See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
 manual.
 ```
 
-## tadaatoolbox (0.14.0)
+## tadaatoolbox (0.15.0)
 Maintainer: Lukas Burk <lukas@quantenbrot.de>  
 Bug reports: https://github.com/tadaadata/tadaatoolbox/issues
 
-0 errors | 0 warnings | 1 note 
-
-```
-checking Rd cross-references ... NOTE
-Package unavailable to check Rd xrefs: ‘rmdformats’
-```
+0 errors | 0 warnings | 0 notes
 
 ## valr (0.3.1)
 Maintainer: Jay Hesselberth <jay.hesselberth@gmail.com>  

diff --git a/revdep/checks.rds b/revdep/checks.rds