REVDEP: Reinstalled all packages for R 3.3.3 and the previous errors …

…when away
HenrikBengtsson · Mar 10, 2017 · f9ff3a0 · f9ff3a0
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diff --git a/revdep/README.md b/revdep/README.md
@@ -14,9 +14,9 @@
 
 ## Packages
 
-|package |*  |version |date       |source        |
-|:-------|:--|:-------|:----------|:-------------|
-|globals |   |0.8.0   |2017-01-17 |cran (@0.8.0) |
+|package |*  |version    |date       |source                             |
+|:-------|:--|:----------|:----------|:----------------------------------|
+|globals |   |0.8.0-9000 |2017-03-10 |local (HenrikBengtsson/globals@NA) |
 
 # Check results
 
@@ -40,9 +40,9 @@
 |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   |      2|        2|     1|
+|PureCN               |1.2.3   |      0|        0|     1|
 |QDNAseq              |1.10.0  |      0|        0|     0|
-|Repitools            |1.20.0  |      2|        1|     2|
+|Repitools            |1.20.0  |      0|        0|     2|
 |R.filesets           |2.11.0  |      0|        0|     0|
 |TIN                  |1.6.0   |      0|        0|     2|
 
@@ -73,7 +73,7 @@ Bug reports: https://github.com/HenrikBengtsson/aroma.core/issues
 ```
 checking package dependencies ... NOTE
 Packages suggested but not available for checking:
-  ‘sfit’ ‘expectile’ ‘HaarSeg’ ‘mpcbs’
+  ‘png’ ‘Cairo’ ‘EBImage’ ‘sfit’ ‘expectile’ ‘HaarSeg’ ‘mpcbs’
 ```
 
 ## calmate (0.12.1)
@@ -281,75 +281,9 @@ Bug reports: https://github.com/HenrikBengtsson/PSCBS/issues
 ## PureCN (1.2.3)
 Maintainer: Markus Riester <markus.riester@novartis.com>
 
-2 errors | 2 warnings | 1 note 
+0 errors | 0 warnings | 1 note 
 
 ```
-checking examples ... ERROR
-Running examples in ‘PureCN-Ex.R’ failed
-The error most likely occurred in:
-
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
-> ### Name: callLOH
-> ### Title: Get regions of LOH
-> ### Aliases: callLOH
-> 
-> ### ** Examples
-> 
-> data(purecn.example.output)
-> head(callLOH(purecn.example.output))
-Error in c(x, values) : 
-  could not find symbol "recursive" in environment of the generic function
-Calls: head -> callLOH -> .getArmLocations
-Execution halted
-
-checking tests ... ERROR
-  Running ‘runTests.R’ [35s/35s]
-Running the tests in ‘tests/runTests.R’ failed.
-Last 13 lines of output:
-       test_predictSomatic 
-  
-     test_runAbsoluteCN.R 
-       test_runAbsoluteCN 
-  
-     test_setMappingBiasVcf.R 
-       test_setMappingBiasVcf 
-  
-     test_setPriorVcf.R 
-       test_setPriorVcf 
-  
-  
-  Error in BiocGenerics:::testPackage("PureCN") : 
-    unit tests failed for package PureCN
-  Execution halted
-
-checking whether package ‘PureCN’ can be installed ... WARNING
-Found the following significant warnings:
-  Warning: namespace ‘Matrix’ is not available and has been replaced
-See ‘/home/hb/repositories/globals/revdep/checks/PureCN.Rcheck/00install.out’ for details.
-
-checking re-building of vignette outputs ... WARNING
-Error in re-building vignettes:
-  ...
-Loading required package: IRanges
-Loading required package: GenomicRanges
-Loading required package: SummarizedExperiment
-Loading required package: Biobase
-Welcome to Bioconductor
-
-    Vignettes contain introductory material; view with
-... 8 lines ...
-
-Attaching package: 'VariantAnnotation'
-
-The following object is masked from 'package:base':
-
-    tabulate
-
-Quitting from lines 382-391 (PureCN.Rnw) 
-Error: processing vignette 'PureCN.Rnw' failed with diagnostics:
-could not find symbol "recursive" in environment of the generic function
-Execution halted
-
 checking R code for possible problems ... NOTE
 Found the following calls to data() loading into the global environment:
 File ‘PureCN/R/bootstrapResults.R’:
@@ -382,75 +316,9 @@ Bug reports: https://github.com/ccagc/QDNAseq/issues
 ## Repitools (1.20.0)
 Maintainer: Mark Robinson <mark.robinson@imls.uzh.ch>
 
-2 errors | 1 warning  | 2 notes
+0 errors | 0 warnings | 2 notes
 
 ```
-checking examples ... ERROR
-Running examples in ‘Repitools-Ex.R’ failed
-The error most likely occurred in:
-
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
-> ### Name: BayMethList
-> ### Title: Class '"BayMethList"'
-> ### Aliases: BayMethList BayMethList-class
-> ###   BayMethList,GRanges,matrix,matrix,numeric-method
-> ###   [,BayMethList,ANY,missing,ANY-method length length,BayMethList-method
-... 50 lines ...
-
-Attaching package: ‘rtracklayer’
-
-The following object is masked from ‘package:Repitools’:
-
-    blocks
-
-Error in .Primitive("c")(<S4 object of class "GRanges">) : 
-  could not find symbol "recursive" in environment of the generic function
-Calls: genomeBlocks ... genomeBlocks -> .local -> genomeBlocks -> genomeBlocks -> .local
-Execution halted
-
-checking tests ... ERROR
-  Running ‘tests.R’ [17s/17s]
-Running the tests in ‘tests/tests.R’ failed.
-Last 13 lines of output:
-  > correctLookupTable[4, c(45, 46)] <- 1
-  > correctLookupTable[4, c(55, 56)] <- 4
-  > correctLookupTable[6, c(49, 50)] <- 6
-  > correctLookupTable[6, c(51, 52)] <- 7
-  > 
-  > if(!all(lookupTable == correctLookupTable, na.rm = TRUE))
-  +     stop("Error in makeWindowLookupTable function")
-  > cat("makeWindowLookupTable tested fine.\n")
-  makeWindowLookupTable tested fine.
-  > 
-  > cpgDensity <- cpgDensityCalc(genes, organism = Hsapiens, window = 500, w.function="linear")
-  Error in .Primitive("c")(<S4 object of class "IRanges">, <S4 object of class "IRanges">,  : 
-    could not find symbol "recursive" in environment of the generic function
-  Calls: cpgDensityCalc ... compress_listData -> do.call -> do.call -> <Anonymous>
-  Execution halted
-
-checking re-building of vignette outputs ... WARNING
-Error in re-building vignettes:
-  ...
-
-    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
-    clusterExport, clusterMap, parApply, parCapply, parLapply,
-    parLapplyLB, parRapply, parSapply, parSapplyLB
-
-The following objects are masked from ‘package:stats’:
-
-... 8 lines ...
-    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
-    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
-    unique, unsplit, which, which.max, which.min
-
-Counting clusters at cutoff -2
-
-Error: processing vignette 'Repitools_vignette.Rnw' failed with diagnostics:
- chunk 2 (label = findClusters) 
-Error in c(query, subject) : 
-  could not find symbol "recursive" in environment of the generic function
-Execution halted
-
 checking R code for possible problems ... NOTE
 Found an obsolete/platform-specific call in the following function:
   ‘maskOut’

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