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291 changes: 291 additions & 0 deletions revdep/README.md
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# Setup

## Platform

|setting |value |
|:--------|:--------------------------------------|
|version |R version 3.3.2 RC (2016-10-26 r71594) |
|system |x86_64, darwin13.4.0 |
|ui |X11 |
|language |(EN) |
|collate |en_US.UTF-8 |
|tz |America/New_York |
|date |2017-04-20 |

## Packages

|package |* |version |date |source |
|:--------|:--|:----------|:----------|:--------------------------------|
|aws.s3 | |0.2.2 |2017-04-20 |Github (cloudyr/aws.s3@305e9da) |
|covr | |2.2.2 |2017-04-20 |Github (jimhester/covr@accef86) |
|digest | |0.6.12 |2017-01-27 |cran (@0.6.12) |
|httr | |1.2.1 |2016-07-03 |cran (@1.2.1) |
|memoise | |1.0.0 |2016-01-29 |cran (@1.0.0) |
|testthat | |1.0.2.9000 |2017-03-03 |Github (hadley/testthat@b72a228) |

# Check results

21 packages

|package |version | errors| warnings| notes|
|:--------------|:-------|------:|--------:|-----:|
|biolink |0.1.2 | 1| 0| 0|
|BWStest |0.2.1 | 0| 0| 0|
|covr |2.2.2 | 0| 0| 0|
|devtools |1.12.0 | 0| 0| 0|
|functools |0.2.0 | 0| 0| 0|
|GSED |1.3 | 0| 0| 0|
|gWidgets2RGtk2 |1.0-5 | 1| 0| 0|
|gWidgets2tcltk |1.0-5 | 1| 0| 0|
|heemod |0.9.0 | 0| 0| 0|
|icd9 |1.3.1 | 0| 0| 1|
|opencage |0.1.0 | 0| 0| 0|
|OpenML |1.3 | 0| 0| 0|
|prcbench |0.7.3 | 0| 0| 1|
|regioneR |1.6.2 | 0| 1| 4|
|rgho |1.0.1 | 0| 0| 0|
|RSQLite |1.1-2 | 0| 0| 0|
|saeRobust |0.1.0 | 0| 0| 0|
|SamplingStrata |1.1 | 0| 0| 0|
|SIDES |1.10 | 0| 0| 0|
|surveillance |1.13.0 | 0| 0| 2|
|toaster |0.5.5 | 0| 0| 0|

## biolink (0.1.2)
Maintainer: Aaron Wolen <[email protected]>

1 error | 0 warnings | 0 notes

```
checking tests ... ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
}) at /private/var/folders/dt/r5s12t392tb5sk181j3gs4zw0000gn/T/RtmpbeCFhk/devtools231b7fa9df2a/lintr/R/object_usage_linter.R:28
18: FUN(X[[i]], ...)
19: codetools::findFuncLocals(formals(fun), body(fun)) at /private/var/folders/dt/r5s12t392tb5sk181j3gs4zw0000gn/T/RtmpbeCFhk/devtools231b7fa9df2a/lintr/R/object_usage_linter.R:53
20: findLocalsList(c(list(body), dropMissings(formals)))
21: body(fun)
22: get(fun, mode = "function", envir = parent.frame())
testthat results ================================================================
OK: 138 SKIPPED: 0 FAILED: 1
1. Error: Package Style (@test-style.r#4)
Error: testthat unit tests failed
Execution halted
```

## BWStest (0.2.1)
Maintainer: Steven E. Pav <[email protected]>
Bug reports: https://github.com/shabbychef/BWStest/issues

0 errors | 0 warnings | 0 notes

## covr (2.2.2)
Maintainer: Jim Hester <[email protected]>
Bug reports: https://github.com/jimhester/covr/issues

0 errors | 0 warnings | 0 notes

## devtools (1.12.0)
Maintainer: Hadley Wickham <[email protected]>
Bug reports: https://github.com/hadley/devtools/issues

0 errors | 0 warnings | 0 notes

## functools (0.2.0)
Maintainer: Paul Hendricks <[email protected]>
Bug reports: https://github.com/paulhendricks/functools/issues

0 errors | 0 warnings | 0 notes

## GSED (1.3)
Maintainer: Marie-Karelle Riviere <[email protected]>

0 errors | 0 warnings | 0 notes

## gWidgets2RGtk2 (1.0-5)
Maintainer: John Verzani <[email protected]>

1 error | 0 warnings | 0 notes

```
checking package dependencies ... ERROR
Package required but not available: ‘RGtk2’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
```

## gWidgets2tcltk (1.0-5)
Maintainer: John Verzani <[email protected]>

1 error | 0 warnings | 0 notes

```
checking whether package ‘gWidgets2tcltk’ can be installed ... ERROR
Installation failed.
See ‘/Users/jhester/Dropbox/projects/memoise/revdep/checks/gWidgets2tcltk.Rcheck/00install.out’ for details.
```

## heemod (0.9.0)
Maintainer: Antoine Filipovic-Pierucci <[email protected]>
Bug reports: https://github.com/pierucci/heemod/issues

0 errors | 0 warnings | 0 notes

## icd9 (1.3.1)
Maintainer: Jack O. Wasey <[email protected]>
Bug reports: https://github.com/jackwasey/icd9/issues

0 errors | 0 warnings | 1 note

```
checking dependencies in R code ... NOTE
Missing or unexported object: ‘devtools::load_data’
```

## opencage (0.1.0)
Maintainer: Maëlle Salmon <[email protected]>
Bug reports: http://github.com/ropenscilabs/opencage/issues

0 errors | 0 warnings | 0 notes

## OpenML (1.3)
Maintainer: Giuseppe Casalicchio <[email protected]>
Bug reports: https://github.com/openml/openml-r/issues

0 errors | 0 warnings | 0 notes

## prcbench (0.7.3)
Maintainer: Takaya Saito <[email protected]>
Bug reports: https://github.com/takayasaito/prcbench/issues

0 errors | 0 warnings | 1 note

```
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘PerfMeas’
```

## regioneR (1.6.2)
Maintainer: Bernat Gel <[email protected]>

0 errors | 1 warning | 4 notes

```
checking whether package ‘regioneR’ can be installed ... WARNING
Found the following significant warnings:
Warning: package ‘S4Vectors’ was built under R version 3.3.3
Warning: package ‘IRanges’ was built under R version 3.3.3
See ‘/Users/jhester/Dropbox/projects/memoise/revdep/checks/regioneR.Rcheck/00install.out’ for details.
checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘memoise’ ‘GenomicRanges’ ‘BSgenome’ ‘rtracklayer’ ‘parallel’
A package should be listed in only one of these fields.
checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
print.permTestResults
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
checking R code for possible problems ... NOTE
commonRegions: no visible global function definition for ‘hasArg’
(/Users/jhester/Dropbox/projects/memoise/revdep/checks/regioneR.Rcheck/00_pkg_src/regioneR/R/commonRegions.R:38)
commonRegions: no visible global function definition for ‘hasArg’
(/Users/jhester/Dropbox/projects/memoise/revdep/checks/regioneR.Rcheck/00_pkg_src/regioneR/R/commonRegions.R:39)
createFunctionsList: no visible global function definition for ‘hasArg’
(/Users/jhester/Dropbox/projects/memoise/revdep/checks/regioneR.Rcheck/00_pkg_src/regioneR/R/createFunctionsList.R:47)
createFunctionsList: no visible global function definition for ‘hasArg’
(/Users/jhester/Dropbox/projects/memoise/revdep/checks/regioneR.Rcheck/00_pkg_src/regioneR/R/createFunctionsList.R:48)
createFunctionsList: no visible global function definition for ‘hasArg’
... 109 lines ...
uniqueRegions: no visible global function definition for ‘hasArg’
(/Users/jhester/Dropbox/projects/memoise/revdep/checks/regioneR.Rcheck/00_pkg_src/regioneR/R/uniqueRegions.R:37)
uniqueRegions: no visible global function definition for ‘hasArg’
(/Users/jhester/Dropbox/projects/memoise/revdep/checks/regioneR.Rcheck/00_pkg_src/regioneR/R/uniqueRegions.R:38)
Undefined global functions or variables:
hasArg is queryHits read.csv read.delim subjectHits
Consider adding
importFrom("methods", "hasArg", "is")
importFrom("utils", "read.csv", "read.delim")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
checking Rd line widths ... NOTE
Rd file 'circularRandomizeRegions.Rd':
\usage lines wider than 90 characters:
circularRandomizeRegions(A, genome="hg19", mask=NULL, max.mask.overlap=NULL, max.retries=10, verbose=TRUE, ...)
Rd file 'commonRegions.Rd':
\examples lines wider than 100 characters:
plotRegions(list(A, B, commons), chromosome="chr1", regions.labels=c("A", "B", "common"), regions.colors=3:1)
Rd file 'createFunctionsList.Rd':
... 95 lines ...
plotRegions(list(A, B, splits), chromosome=1, regions.labels=c("A", "B", "splits"), regions.colors=3:1)
Rd file 'subtractRegions.Rd':
\examples lines wider than 100 characters:
plotRegions(list(A, B, subtract), chromosome=1, regions.labels=c("A", "B", "subtract"), regions.colors=3:1)
Rd file 'uniqueRegions.Rd':
\examples lines wider than 100 characters:
plotRegions(list(A, B, uniques), chromosome="chr1", regions.labels=c("A", "B", "uniques"), regions.colors=3:1)
These lines will be truncated in the PDF manual.
```

## rgho (1.0.1)
Maintainer: Antoine Filipovic-Pierucci <[email protected]>
Bug reports: https://github.com/pierucci/rgho/issues

0 errors | 0 warnings | 0 notes

## RSQLite (1.1-2)
Maintainer: Kirill Müller <[email protected]>
Bug reports: https://github.com/rstats-db/RSQLite/issues

0 errors | 0 warnings | 0 notes

## saeRobust (0.1.0)
Maintainer: Sebastian Warnholz <[email protected]>
Bug reports: https://github.com/wahani/saeRobust/issues

0 errors | 0 warnings | 0 notes

## SamplingStrata (1.1)
Maintainer: Giulio Barcaroli <[email protected]>

0 errors | 0 warnings | 0 notes

## SIDES (1.10)
Maintainer: Marie-Karelle Riviere <[email protected]>

0 errors | 0 warnings | 0 notes

## surveillance (1.13.0)
Maintainer: Sebastian Meyer <[email protected]>
Bug reports: https://r-forge.r-project.org/tracker/?group_id=45

0 errors | 0 warnings | 2 notes

```
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘INLA’
checking installed package size ... NOTE
installed size is 9.6Mb
sub-directories of 1Mb or more:
R 4.2Mb
doc 2.3Mb
```

## toaster (0.5.5)
Maintainer: Gregory Kanevsky <[email protected]>
Bug reports: https://github.com/teradata-aster-field/toaster/issues

0 errors | 0 warnings | 0 notes

6 changes: 3 additions & 3 deletions revdep/check.R
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library("devtools")

res <- revdep_check(bioconductor = TRUE, threads = 4)
revdep_check_save_summary(res)
revdep_check_save_logs(res)
revdep_check_resume(bioconductor = TRUE)
revdep_check_save_summary()
revdep_check_print_problems()
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