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REVDEP: Reran reverse package dependency checks on 32 (was 23) packag…
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…es (Issue #27)
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@HenrikBengtsson
HenrikBengtsson committed Jun 30, 2017
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216 changes: 148 additions & 68 deletions revdep/README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -4,49 +4,58 @@

|setting |value |
|:--------|:----------------------------|
|version |R version 3.3.3 (2017-03-06) |
|version |R version 3.4.0 (2017-04-21) |
|system |x86_64, linux-gnu |
|ui |X11 |
|language |en |
|collate |en_US.UTF-8 |
|tz |America/Los_Angeles |
|date |2017-04-16 |
|date |2017-06-29 |

## Packages

|package |* |version |date |source |
|:-------|:--|:-------|:----------|:-------------|
|globals | |0.9.0 |2017-03-10 |cran (@0.9.0) |
|package |* |version |date |source |
|:-------|:--|:-------|:----------|:--------------|
|globals | |0.10.0 |2017-04-17 |cran (@0.10.0) |

# Check results

23 packages

|package |version | errors| warnings| notes|
|:--------------------|:-------|------:|--------:|-----:|
|ACNE |0.8.1 | 0| 0| 0|
|aroma.affymetrix |3.1.0 | 0| 0| 0|
|aroma.cn |1.6.1 | 0| 0| 0|
|aroma.core |3.1.0 | 0| 0| 0|
|calmate |0.12.1 | 0| 0| 0|
|doFuture |0.5.0 | 0| 0| 0|
|fiery |0.2.2 | 0| 0| 0|
|future.BatchJobs |0.14.0 | 0| 0| 0|
|future |1.4.0 | 0| 0| 0|
|GeneBreak |1.4.0 | 0| 0| 1|
|googleComputeEngineR |0.1.0 | 0| 0| 0|
|MPAgenomics |1.1.2 | 0| 0| 2|
|NSA |0.0.32 | 0| 0| 6|
|pbmcapply |1.2.1 | 0| 0| 0|
|PECA |1.10.0 | 0| 0| 1|
|PSCBS |0.62.0 | 0| 0| 0|
|PureCN |1.2.3 | 0| 0| 1|
|QDNAseq |1.10.0 | 0| 0| 0|
|Repitools |1.20.0 | 0| 0| 2|
|R.filesets |2.11.0 | 0| 0| 0|
|TIN |1.6.0 | 0| 0| 2|
|vesselr |0.2.1 | 0| 0| 0|
|warbleR |1.1.6 | 0| 0| 0|
32 packages

|package |version | errors| warnings| notes|
|:--------------------|:----------|------:|--------:|-----:|
|ACNE |0.8.1 | 0| 0| 0|
|aroma.affymetrix |3.1.0 | 0| 0| 0|
|aroma.cn |1.6.1 | 0| 0| 0|
|aroma.core |3.1.0 | 0| 0| 1|
|calmate |0.12.1 | 0| 0| 0|
|doFuture |0.5.0 | 0| 0| 0|
|easyml |0.1.0 | 0| 0| 0|
|fiery |0.2.3 | 0| 0| 0|
|future.BatchJobs |0.14.1 | 0| 0| 0|
|future.batchtools |0.5.0 | 0| 0| 0|
|future |1.5.0 | 0| 0| 0|
|GeneBreak |1.6.0 | 0| 0| 1|
|googleComputeEngineR |0.1.0 | 0| 0| 0|
|kernelboot |0.1.1 | 0| 0| 0|
|MPAgenomics |1.1.2 | 0| 0| 2|
|NSA |0.0.32 | 0| 0| 6|
|origami |0.8.0 | 0| 0| 0|
|pbmcapply |1.2.2 | 0| 0| 0|
|PeakSegDP |2017.06.20 | 0| 0| 0|
|PeakSegOptimal |2017.06.20 | 0| 0| 1|
|PECA |1.12.0 | 0| 0| 1|
|penaltyLearning |2017.06.14 | 0| 0| 0|
|PSCBS |0.63.0 | 0| 0| 0|
|PureCN |1.6.3 | 0| 0| 1|
|QDNAseq |1.12.0 | 0| 1| 0|
|Repitools |1.22.0 | 0| 0| 3|
|R.filesets |2.11.0 | 0| 0| 0|
|sperrorest |2.0.0 | 0| 0| 0|
|startR |0.0.1 | 0| 0| 0|
|TIN |1.8.0 | 0| 0| 2|
|vesselr |0.2.1 | 0| 0| 0|
|warbleR |1.1.8 | 0| 0| 0|

## ACNE (0.8.1)
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Expand All @@ -70,7 +79,13 @@ Bug reports: https://github.com/HenrikBengtsson/aroma.cn/issues
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Bug reports: https://github.com/HenrikBengtsson/aroma.core/issues

0 errors | 0 warnings | 0 notes
0 errors | 0 warnings | 1 note

```
checking package dependencies ... NOTE
Packages suggested but not available for checking:
‘expectile’ ‘HaarSeg’ ‘mpcbs’
```

## calmate (0.12.1)
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Expand All @@ -84,25 +99,37 @@ Bug reports: https://github.com/HenrikBengtsson/doFuture/issues

0 errors | 0 warnings | 0 notes

## fiery (0.2.2)
## easyml (0.1.0)
Maintainer: Woo-Young Ahn <ahn.280@osu.edu>
Bug reports: https://github.com/CCS-Lab/easyml/issues

0 errors | 0 warnings | 0 notes

## fiery (0.2.3)
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Bug reports: https://github.com/thomasp85/fiery/issues

0 errors | 0 warnings | 0 notes

## future.BatchJobs (0.14.0)
## future.BatchJobs (0.14.1)
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Bug reports: https://github.com/HenrikBengtsson/future.BatchJobs/issues

0 errors | 0 warnings | 0 notes

## future (1.4.0)
## future.batchtools (0.5.0)
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Bug reports: https://github.com/HenrikBengtsson/future.batchtools/issues

0 errors | 0 warnings | 0 notes

## future (1.5.0)
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Bug reports: https://github.com/HenrikBengtsson/future/issues

0 errors | 0 warnings | 0 notes

## GeneBreak (1.4.0)
## GeneBreak (1.6.0)
Maintainer: Evert van den Broek <vandenbroek.evert@gmail.com>

0 errors | 0 warnings | 1 note
Expand Down Expand Up @@ -131,6 +158,12 @@ Bug reports: https://github.com/cloudyr/googleComputeEngineR/issues

0 errors | 0 warnings | 0 notes

## kernelboot (0.1.1)
Maintainer: Tymoteusz Wolodzko <twolodzko+kernelboot@gmail.com>
Bug reports: https://github.com/twolodzko/kernelboot/issues

0 errors | 0 warnings | 0 notes

## MPAgenomics (1.1.2)
Maintainer: Samuel Blanck <samuel.blanck@inria.fr>

Expand Down Expand Up @@ -248,13 +281,41 @@ Rd file 'NSANormalization.Rd':
These lines will be truncated in the PDF manual.
```

## pbmcapply (1.2.1)
## origami (0.8.0)
Maintainer: Jeremy Coyle <jeremyrcoyle@gmail.com>

0 errors | 0 warnings | 0 notes

## pbmcapply (1.2.2)
Maintainer: Kevin kuang <kvn.kuang@mail.utoronto.ca>
Bug reports: https://github.com/kvnkuang/pbmcapply/issues

0 errors | 0 warnings | 0 notes

## PECA (1.10.0)
## PeakSegDP (2017.06.20)
Maintainer: Toby Dylan Hocking <toby.hocking@r-project.org>

0 errors | 0 warnings | 0 notes

## PeakSegOptimal (2017.06.20)
Maintainer: Toby Dylan Hocking <toby.hocking@r-project.org>

0 errors | 0 warnings | 1 note

```
checking compiled code ... NOTE
File ‘PeakSegOptimal/libs/PeakSegOptimal.so’:
Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
Objects: ‘PeakSegFPOPLog.o’, ‘PeakSegPDPALog.o’,
‘funPieceListLog.o’
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
```

## PECA (1.12.0)
Maintainer: Tomi Suomi <tomi.suomi@utu.fi>

0 errors | 0 warnings | 1 note
Expand All @@ -268,51 +329,49 @@ Rd file 'PECA.Rd':
These lines will be truncated in the PDF manual.
```

## PSCBS (0.62.0)
## penaltyLearning (2017.06.14)
Maintainer: Toby Dylan Hocking <toby.hocking@r-project.org>

0 errors | 0 warnings | 0 notes

## PSCBS (0.63.0)
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Bug reports: https://github.com/HenrikBengtsson/PSCBS/issues

0 errors | 0 warnings | 0 notes

## PureCN (1.2.3)
## PureCN (1.6.3)
Maintainer: Markus Riester <markus.riester@novartis.com>

0 errors | 0 warnings | 1 note

```
checking R code for possible problems ... NOTE
Found the following calls to data() loading into the global environment:
File ‘PureCN/R/bootstrapResults.R’:
data(purecn.example.output)
File ‘PureCN/R/callAlterations.R’:
data(purecn.example.output)
data(purecn.example.output)
File ‘PureCN/R/callLOH.R’:
data(purecn.example.output)
File ‘PureCN/R/createCurationFile.R’:
data(purecn.example.output)
File ‘PureCN/R/curateResults.R’:
data(purecn.example.output)
data(purecn.example.output)
File ‘PureCN/R/plotAbs.R’:
data(purecn.example.output)
File ‘PureCN/R/predictSomatic.R’:
data(purecn.example.output)
File ‘PureCN/R/readCurationFile.R’:
data(purecn.example.output)
See section ‘Good practice’ in ‘?data’.
checking installed package size ... NOTE
installed size is 5.6Mb
sub-directories of 1Mb or more:
doc 1.6Mb
extdata 2.7Mb
```

## QDNAseq (1.10.0)
## QDNAseq (1.12.0)
Maintainer: Daoud Sie <d.sie@vumc.nl>
Bug reports: https://github.com/ccagc/QDNAseq/issues

0 errors | 0 warnings | 0 notes
0 errors | 1 warning | 0 notes

```
checking for missing documentation entries ... WARNING
Undocumented code objects:
‘exportVCF’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
```

## Repitools (1.20.0)
## Repitools (1.22.0)
Maintainer: Mark Robinson <mark.robinson@imls.uzh.ch>

0 errors | 0 warnings | 2 notes
0 errors | 0 warnings | 3 notes

```
checking R code for possible problems ... NOTE
Expand Down Expand Up @@ -360,6 +419,15 @@ Rd file 'writeWig.Rd':
writeWig(rs, seq.len = NULL, design=NULL, sample=20, drop.zero=TRUE, normalize=TRUE, verbose=TRUE)
These lines will be truncated in the PDF manual.
checking compiled code ... NOTE
File ‘Repitools/libs/Repitools.so’:
Found no call to: ‘R_useDynamicSymbols’
It is good practice to register native routines and to disable symbol
search.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
```

## R.filesets (2.11.0)
Expand All @@ -368,7 +436,19 @@ Bug reports: https://github.com/HenrikBengtsson/R.filesets/issues

0 errors | 0 warnings | 0 notes

## TIN (1.6.0)
## sperrorest (2.0.0)
Maintainer: Alexander Brenning <alexander.brenning@uni-jena.de>
Bug reports: https://github.com/pat-s/sperrorest/issues

0 errors | 0 warnings | 0 notes

## startR (0.0.1)
Maintainer: Nicolau Manubens <nicolau.manubens@bsc.es>
Bug reports: https://earth.bsc.es/gitlab/es/startR/issues

0 errors | 0 warnings | 0 notes

## TIN (1.8.0)
Maintainer: Bjarne Johannessen <bjajoh@rr-research.no>

0 errors | 0 warnings | 2 notes
Expand Down Expand Up @@ -407,7 +487,7 @@ Maintainer: Jordan D. Dworkin <jdwor@mail.med.upenn.edu>

0 errors | 0 warnings | 0 notes

## warbleR (1.1.6)
## warbleR (1.1.8)
Maintainer: Marcelo Araya-Salas <araya-salas@cornell.edu>
Bug reports: https://github.com/maRce10/warbleR/issues

Expand Down
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28 changes: 22 additions & 6 deletions revdep/problems.md
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Expand Up @@ -4,24 +4,40 @@

|setting |value |
|:--------|:----------------------------|
|version |R version 3.3.3 (2017-03-06) |
|version |R version 3.4.0 (2017-04-21) |
|system |x86_64, linux-gnu |
|ui |X11 |
|language |en |
|collate |en_US.UTF-8 |
|tz |America/Los_Angeles |
|date |2017-04-16 |
|date |2017-06-29 |

## Packages

|package |* |version |date |source |
|:-------|:--|:-------|:----------|:-------------|
|globals | |0.9.0 |2017-03-10 |cran (@0.9.0) |
|package |* |version |date |source |
|:-------|:--|:-------|:----------|:--------------|
|globals | |0.10.0 |2017-04-17 |cran (@0.10.0) |

# Check results

0 packages with problems
1 packages with problems

|package |version | errors| warnings| notes|
|:-------|:-------|------:|--------:|-----:|
|QDNAseq |1.12.0 | 0| 1| 0|

## QDNAseq (1.12.0)
Maintainer: Daoud Sie <d.sie@vumc.nl>
Bug reports: https://github.com/ccagc/QDNAseq/issues

0 errors | 1 warning | 0 notes

```
checking for missing documentation entries ... WARNING
Undocumented code objects:
‘exportVCF’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
```

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R/cleanup.R:12:1: style: Variable or function name should be snake_case.

​cleanup.Globals <- function(globals, drop = c("missing", "base-packages"),
^~~~~~~~~~~~~~~

R/cleanup.R:30:11: warning: no visible global function definition for ‘is_base_pkg’

​      if (is_base_pkg(environmentName(where[[name]]))) keep[name] <- FALSE
          ^~~~~~~~~~~

R/cleanup.R:44:11: warning: no visible global function definition for ‘is_internal’

​      if (is_internal(globals[[name]])) keep[name] <- FALSE
          ^~~~~~~~~~~

R/findGlobals.R:17:10: warning: no visible global function definition for ‘makeUsageCollector’

​    w <- makeUsageCollector(fun, name = "<anonymous>", enterGlobal = enter)
         ^~~~~~~~~~~~~~~~~~

R/findGlobals.R:18:21: warning: no visible global function definition for ‘inject_tracer_to_walker’

​    if (trace) w <- inject_tracer_to_walker(w)
                    ^~~~~~~~~~~~~~~~~~~~~~~

R/findGlobals.R:19:5: warning: no visible global function definition for ‘collect_usage_function’

​    collect_usage_function(fun, name = "<anonymous>", w)
    ^~~~~~~~~~~~~~~~~~~~~~

R/findGlobals.R:22:12: warning: no visible global function definition for ‘as_function’, Did you mean 'as.function'?

​    fun <- as_function(expr, envir = envir, ...)
           ^~~~~~~~~~~

R/findGlobals.R:26:10: warning: no visible global function definition for ‘makeUsageCollector’

​    w <- makeUsageCollector(fun, name = "<anonymous>", enterGlobal = enter)
         ^~~~~~~~~~~~~~~~~~

R/findGlobals.R:28:21: warning: no visible global function definition for ‘inject_tracer_to_walker’

​    if (trace) w <- inject_tracer_to_walker(w)
                    ^~~~~~~~~~~~~~~~~~~~~~~

R/findGlobals.R:29:1: style: Trailing whitespace is superfluous.

​    
^~~~

R/findGlobals.R:30:15: warning: no visible global function definition for ‘findLocalsList’

​    locals <- findLocalsList(list(expr))
              ^~~~~~~~~~~~~~

R/findGlobals.R:32:5: warning: no visible global function definition for ‘walkCode’

​    walkCode(expr, w)
    ^~~~~~~~

R/findGlobals.R:50:10: warning: no visible global function definition for ‘makeUsageCollector’

​    w <- makeUsageCollector(fun, name = "<anonymous>", enterGlobal = enter)
         ^~~~~~~~~~~~~~~~~~

R/findGlobals.R:51:21: warning: no visible global function definition for ‘inject_tracer_to_walker’

​    if (trace) w <- inject_tracer_to_walker(w)
                    ^~~~~~~~~~~~~~~~~~~~~~~

R/findGlobals.R:52:5: warning: no visible global function definition for ‘collect_usage_function’

​    collect_usage_function(fun, name = "<anonymous>", w)
    ^~~~~~~~~~~~~~~~~~~~~~

R/findGlobals.R:54:12: warning: no visible global function definition for ‘as_function’, Did you mean 'as.function'?

​    fun <- as_function(expr, envir = envir, ...)
           ^~~~~~~~~~~

R/findGlobals.R:55:10: warning: no visible global function definition for ‘makeUsageCollector’

​    w <- makeUsageCollector(fun, name = "<anonymous>", enterGlobal = enter)
         ^~~~~~~~~~~~~~~~~~

R/findGlobals.R:56:21: warning: no visible global function definition for ‘inject_tracer_to_walker’

​    if (trace) w <- inject_tracer_to_walker(w)
                    ^~~~~~~~~~~~~~~~~~~~~~~

R/findGlobals.R:57:5: warning: no visible global function definition for ‘walkCode’

​    walkCode(expr, w)
    ^~~~~~~~

R/findGlobals.R:101:21: warning: no visible global function definition for ‘inject_tracer_to_walker’

​    if (trace) w <- inject_tracer_to_walker(w)
                    ^~~~~~~~~~~~~~~~~~~~~~~

R/findGlobals.R:102:5: warning: no visible global function definition for ‘collect_usage_function’

​    collect_usage_function(fun, name = "<anonymous>", w)
    ^~~~~~~~~~~~~~~~~~~~~~

R/findGlobals.R:104:12: warning: no visible global function definition for ‘as_function’, Did you mean 'as.function'?

​    fun <- as_function(expr, envir = envir, ...)
           ^~~~~~~~~~~

R/findGlobals.R:108:21: warning: no visible global function definition for ‘inject_tracer_to_walker’

​    if (trace) w <- inject_tracer_to_walker(w)
                    ^~~~~~~~~~~~~~~~~~~~~~~

R/findGlobals.R:109:5: warning: no visible global function definition for ‘walkCode’

​    walkCode(expr, w)
    ^~~~~~~~

R/findGlobals.R:135:5: warning: no visible global function definition for ‘mdebug’, Did you mean 'debug'?

​    mdebug(" - expr: <a list of length %d>", length(expr))
    ^~~~~~

R/findGlobals.R:168:5: warning: no visible global function definition for ‘mdebug’, Did you mean 'debug'?

​    mdebug(" - tweaking expression using function")
    ^~~~~~

R/findGlobals.R:173:23: warning: no visible binding for global variable ‘find_globals_ordered’

​    find_globals_t <- find_globals_ordered
                      ^~~~~~~~~~~~~~~~~~~~

R/findGlobals.R:175:23: warning: no visible binding for global variable ‘find_globals_conservative’

​    find_globals_t <- find_globals_conservative
                      ^~~~~~~~~~~~~~~~~~~~~~~~~

R/findGlobals.R:177:23: warning: no visible binding for global variable ‘find_globals_liberal’

​    find_globals_t <- find_globals_liberal
                      ^~~~~~~~~~~~~~~~~~~~

R/findGlobals.R:197:7: warning: no visible global function definition for ‘mdebug’, Did you mean 'debug'?

​      mdebug(" - detected: %s", dQuote(trim(w$message)))
      ^~~~~~

R/findGlobals.R:197:40: warning: no visible global function definition for ‘trim’, Did you mean 'arima'?

​      mdebug(" - detected: %s", dQuote(trim(w$message)))
                                       ^~~~

R/findGlobals.R:215:3: warning: no visible global function definition for ‘mdebug’, Did you mean 'debug'?

​  mdebug(" - globals found: [%d] %s", length(globals), hpaste(sQuote(globals)))
  ^~~~~~

R/findGlobals.R:215:56: warning: no visible global function definition for ‘hpaste’, Did you mean 'paste'?

​  mdebug(" - globals found: [%d] %s", length(globals), hpaste(sQuote(globals)))
                                                       ^~~~~~

R/findGlobals.R:243:20: warning: no visible global function definition for ‘drop_missing_formals’

​  formals_clean <- drop_missing_formals(formals)
                   ^~~~~~~~~~~~~~~~~~~~

R/findGlobals.R:244:13: warning: no visible global function definition for ‘findLocalsList’

​  locals <- findLocalsList(c(list(body), formals_clean))
            ^~~~~~~~~~~~~~

R/findGlobals.R:248:28: warning: no visible global function definition for ‘walkCode’

​  for (a in formals_clean) walkCode(a, w)
                           ^~~~~~~~

R/findGlobals.R:250:3: warning: no visible global function definition for ‘walkCode’

​  walkCode(body, w)
  ^~~~~~~~

R/findGlobals.R:257:3: warning: local variable ‘args’ assigned but may not be used

​  args <- setdiff(names(f), c("w", "..."))
  ^~~~

R/findGlobals.R:258:3: warning: local variable ‘title’ assigned but may not be used

​  title <- sprintf("%s():", name)
  ^~~~~

R/findGlobals.R:270:7: style: Variable or function name should be snake_case.

​    w$startCollectLocals <- function(parnames, locals, ...) { NULL }
      ^~~~~~~~~~~~~~~~~~

R/findGlobals.R:273:7: style: Variable or function name should be snake_case.

​    w$finishCollectLocals <- function(w, ...) { NULL }
      ^~~~~~~~~~~~~~~~~~~

R/findGlobals.R:276:7: style: Variable or function name should be snake_case.

​    w$enterInternal <- function(type, v, e, ...) { NULL }
      ^~~~~~~~~~~~~

R/findGlobals.R:278:1: style: Trailing whitespace is superfluous.

​  
^~

R/findGlobals.R:280:20: style: Trailing whitespace is superfluous.

​    fcn <- w[[key]] 
                   ^

R/findGlobals.R:282:12: warning: no visible global function definition for ‘inject_tracer_to_function’

​    fcn <- inject_tracer_to_function(fcn, key)
           ^~~~~~~~~~~~~~~~~~~~~~~~~

R/findGlobals.R:285:1: style: Trailing whitespace is superfluous.

​  
^~

R/Globals-class.R:16:1: style: Variable or function name should be snake_case.

​Globals <- function(object = list(), ...) {
^~~~~~~

R/Globals-class.R:66:3: warning: no visible global function definition for ‘Globals’

​  Globals(x, ...)
  ^~~~~~~

R/Globals-class.R:178:1: style: Variable or function name should be snake_case.

​unique.Globals <- function(x, ...) {
^~~~~~~~~~~~~~

R/globalsOf.R:62:1: style: Variable or function name should be snake_case.

​globalsOf <- function(expr, envir = parent.frame(), ...,
^~~~~~~~~

R/globalsOf.R:64:57: style: Variable or function name should be snake_case.

​                      tweak = NULL, substitute = FALSE, mustExist = TRUE,
                                                        ^~~~~~~~~

R/globalsOf.R:80:5: warning: no visible global function definition for ‘globalsByName’

​    globalsByName(names, envir = envir, mustExist = mustExist)
    ^~~~~~~~~~~~~

R/globalsOf.R:95:5: warning: no visible global function definition for ‘mdebug’, Did you mean 'debug'?

​    mdebug(" - recursive scan of preliminary globals ...")
    ^~~~~~

R/globalsOf.R:100:34: warning: no visible binding for global variable ‘envname’, Did you mean 'unname'?

​    where <- sapply(where, FUN = envname)
                                 ^~~~~~~

R/globalsOf.R:115:9: warning: no visible global function definition for ‘mdebug’, Did you mean 'debug'?

​        mdebug("   + scanning global #%d (%s) ...", gg, sQuote(names_t[[gg]]))
        ^~~~~~

R/globalsOf.R:130:7: warning: no visible global function definition for ‘mdebug’, Did you mean 'debug'?

​      mdebug(" - subset of globals to be scanned: [0]")
      ^~~~~~

R/globalsOf.R:133:5: warning: no visible global function definition for ‘mdebug’, Did you mean 'debug'?

​    mdebug(" - recursive scan of preliminary globals ... DONE")
    ^~~~~~

R/globalsOf.R:159:1: style: Variable or function name should be snake_case.

​globalsByName <- function(names, envir = parent.frame(), mustExist = TRUE,
^~~~~~~~~~~~~

R/globalsOf.R:159:58: style: Variable or function name should be snake_case.

​globalsByName <- function(names, envir = parent.frame(), mustExist = TRUE,
                                                         ^~~~~~~~~

R/globalsOf.R:165:3: warning: no visible global function definition for ‘mdebug’, Did you mean 'debug'?

​  mdebug("- search from environment: %s", sQuote(envname(envir)))
  ^~~~~~

R/globalsOf.R:165:50: warning: no visible global function definition for ‘envname’, Did you mean 'unname'?

​  mdebug("- search from environment: %s", sQuote(envname(envir)))
                                                 ^~~~~~~

R/globalsOf.R:171:3: warning: no visible global function definition for ‘mdebug’, Did you mean 'debug'?

​  mdebug("- dotdotdot: %s", needs_dotdotdot)
  ^~~~~~

R/globalsOf.R:177:5: warning: no visible global function definition for ‘mdebug’, Did you mean 'debug'?

​    mdebug("- locating #%d (%s)", kk, sQuote(name))
    ^~~~~~

R/globalsOf.R:179:5: warning: no visible global function definition for ‘mdebug’, Did you mean 'debug'?

​    mdebug("  + found in environment: %s", sQuote(envname(env)))
    ^~~~~~

R/globalsOf.R:179:51: warning: no visible global function definition for ‘envname’, Did you mean 'unname'?

​    mdebug("  + found in environment: %s", sQuote(envname(env)))
                                                  ^~~~~~~

R/packagesOf.R:2:1: style: Variable or function name should be snake_case.

​packagesOf <- function(...) UseMethod("packagesOf")
^~~~~~~~~~

R/packagesOf.R:13:1: style: Variable or function name should be snake_case.

​packagesOf.Globals <- function(globals, ...) {
^~~~~~~~~~~~~~~~~~

R/utils.R:19:13: warning: no visible global function definition for ‘find_base_pkgs’

​  pkgs %in% find_base_pkgs()
            ^~~~~~~~~~~~~~

R/utils.R:25:3: warning: no visible global function definition for ‘is_base_pkg’

​  is_base_pkg(environmentName(environment(x)))
  ^~~~~~~~~~~

R/walkAST.R:17:1: style: Variable or function name should be snake_case.

​walkAST <- function(expr, atomic = NULL, name = NULL, call = NULL,
^~~~~~~

R/walkAST.R:71:5: style: Variable or function name should be snake_case.

​    onUnknownType <- getOption("globals.walkAST.onUnknownType", "error")
    ^~~~~~~~~~~~~

R/where.R:25:7: warning: no visible global function definition for ‘mdebug’, Did you mean 'debug'?

​      mdebug("  + found in location: %s", sQuote(envname(env)))
      ^~~~~~

R/where.R:25:50: warning: no visible global function definition for ‘envname’, Did you mean 'unname'?

​      mdebug("  + found in location: %s", sQuote(envname(env)))
                                                 ^~~~~~~

R/where.R:31:7: warning: no visible global function definition for ‘mdebug’, Did you mean 'debug'?

​      mdebug("  + failed to located: NULL")
      ^~~~~~

R/where.R:39:3: warning: no visible global function definition for ‘mdebug’, Did you mean 'debug'?

​  mdebug("- failed to located: NULL")
  ^~~~~~

tests/dotdotdot.R:150:14: warning: no visible global function definition for ‘globalsOf’, Did you mean 'globals'?

​  globals <- globalsOf(expr, dotdotdot = "ignore")
             ^~~~~~~~~

tests/dotdotdot.R:159:14: warning: no visible global function definition for ‘globalsOf’, Did you mean 'globals'?

​  globals <- globalsOf(expr, dotdotdot = "return")
             ^~~~~~~~~

tests/dotdotdot.R:173:14: warning: no visible global function definition for ‘globalsOf’, Did you mean 'globals'?

​  globals <- globalsOf(expr, dotdotdot = "warn")
             ^~~~~~~~~

tests/dotdotdot.R:187:18: warning: no visible global function definition for ‘globalsOf’, Did you mean 'globals'?

​  globals <- try(globalsOf(expr, dotdotdot = "error"))
                 ^~~~~~~~~

tests/dotdotdot.R:199:12: warning: no visible global function definition for ‘globalsOf’, Did you mean 'globals'?

​globals <- globalsOf(exprs, dotdotdot = "return")
           ^~~~~~~~~

tests/formulas.R:19:3: warning: no visible global function definition for ‘map’, Did you mean 'mad'?

​  map(1L, ~ typeof(x + .x))
  ^~~

tests/globalsOf.R:34:24: style: Variable or function name should be snake_case.

​  substitute({ x <- B; B <- 1; y <- C; z <- D }, env = list())
                       ^

tests/walkAST.R:93:1: style: Trailing whitespace is superfluous.

​  
^~

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