Re: [Bioc-devel] select(Homo.sapiens,...) failing

[Vincent Carey]

Thanks Val that did the trick.

On Mon, May 2, 2016 at 4:40 PM, Obenchain, Valerie <
valerie.obench...@roswellpark.org> wrote:

> Hi Vince,
>
> You need version >=1.13.9 of OrganismDbi. Unfortunately it's failing
> check because of the biomart problems so you'll have to get it from svn.
> Let me know if you still have problems after updating.
>
> Val
>
>
> On 05/02/2016 11:53 AM, Vincent Carey wrote:
> > biocValid() says all is well ...
> >
> >> select(Homo.sapiens, keys="1001", keytype="ENTREZID", columns="SYMBOL")
> > *Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : *
> >
> > *  object '.testSelectArgs' not found*
> >
> >> sessionInfo()
> > R version 3.3.0 beta (2016-04-01 r70412)
> >
> > Platform: x86_64-apple-darwin13.4.0 (64-bit)
> >
> > Running under: OS X 10.10.5 (Yosemite)
> >
> >
> > locale:
> >
> > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> >
> >
> > attached base packages:
> >
> > [1] parallel  stats4stats graphics  grDevices utils datasets
> >
> > [8] methods   base
> >
> >
> > other attached packages:
> >
> >  [1] Homo.sapiens_1.3.1
> >
> >  [2] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
> >
> >  [3] org.Hs.eg.db_3.3.0
> >
> >  [4] GO.db_3.3.0
> >
> >  [5] OrganismDbi_1.13.8
> >
> >  [6] GenomicFeatures_1.23.31
> >
> >  [7] GenomicRanges_1.23.27
> >
> >  [8] GenomeInfoDb_1.7.6
> >
> >  [9] AnnotationDbi_1.33.15
> >
> > [10] IRanges_2.5.46
> >
> >
> > [11] S4Vectors_0.9.52
> >
> > [12] Biobase_2.31.3
> >
> > [13] BiocGenerics_0.17.5
> >
> > [14] BiocInstaller_1.21.6
> >
> >
> > loaded via a namespace (and not attached):
> >
> >  [1] graph_1.49.1Rcpp_0.12.4.5
> >
> >  [3] XVector_0.11.8  zlibbioc_1.17.1
> >
> >  [5] GenomicAlignments_1.7.21BiocParallel_1.5.22
> >
> >  [7] tools_3.3.0 SummarizedExperiment_1.1.27
> >
> >  [9] DBI_0.4 RBGL_1.47.0
> >
> > [11] rtracklayer_1.31.11 bitops_1.0-6
> >
> > [13] RCurl_1.95-4.8  biomaRt_2.27.2
> >
> > [15] RSQLite_1.0.0   Biostrings_2.39.14
> >
> > [17] Rsamtools_1.23.11   XML_3.98-1.4
> >
> >   [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
>
>
> This email message may contain legally privileged and/or confidential
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Re: [Bioc-devel] How to debug for the warnings?

[Martin Morgan]

On 05/02/2016 05:53 PM, Ou, Jianhong wrote:

Hi All,


I got some warnings when check. However, I could not see any details for that 
warnings. How could I debug for these kind of warnings? Thank you.


Please see this thread

https://stat.ethz.ch/pipermail/bioc-devel/2016-May/009205.html

and update BiocInstaller (from svn)

svn co 
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BiocInstaller





* using log directory �/home/biocbuild/bbs-3.3-bioc/meat/ChIPpeakAnno.Rcheck�
* using R version 3.3.0 RC (2016-04-25 r70549)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option �--no-vignettes�
* checking for file �ChIPpeakAnno/DESCRIPTION� ... OK
* checking extension type ... Package
* this is package �ChIPpeakAnno� version �3.5.18�
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
   �grid� �IRanges� �Biostrings� �GenomicRanges� �S4Vectors�
   �VennDiagram�
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package �ChIPpeakAnno� can be installed ... [20s/22s] OK
* checking installed package size ... NOTE
   installed size is 19.4Mb
   sub-directories of 1Mb or more:
 data 12.7Mb
 extdata   5.2Mb
* checking package directory ... OK
* checking �build� directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE

* checking S3 generic/method consistency ... WARNING

See section �Generic functions and methods� in the �Writing R
Extensions� manual.
* checking replacement functions ... WARNING

The argument of a replacement function which corresponds to the right
hand side must be named �value�.
* checking foreign function calls ... NOTE

See chapter �System and foreign language interfaces� in the �Writing R
Extensions� manual.
* checking R code for possible problems ... NOTE
BED2RangedData: no visible global function definition for 'read.delim'
GFF2RangedData: no visible global function definition for 'read.delim'
addGeneIDs : is.installed: no visible global function definition for
   'installed.packages'
binOverFeature: no visible global function definition for 'par'
binOverFeature : plotErrBar: no visible global function definition for
   'segments'
binOverFeature : plotErrBar: no visible global function definition for
   'par'
binOverFeature : : no visible global function definition for
   'plot'
binOverFeature : : no visible global function definition for
   'abline'
binOverFeature : : no visible global function definition for
   'axis'
buildBindingDistribution: no visible global function definition for
   'boxplot.stats'
buildBindingDistribution: no visible global function definition for
   'hist'
df2GRanges : : no visible global function definition for
   'rgb'
egOrgMap: no visible global function definition for 'adist'
featureAlignedDistribution: no visible global function definition for
   'matplot'
featureAlignedDistribution: no visible global function definition for
   'axis'
featureAlignedDistribution: no visible global function definition for
   'legend'
featureAlignedHeatmap: no visible global function definition for
   'colorRampPalette'
featureAlignedHeatmap : areColors : : no visible global
   function definition for 'col2rgb'
findOverlappingPeaks : : no visible binding for global
   variable 'data'
makeVennDiagram : plotVenn: no visible global function definition for
   'par'
makeVennDiagram : plotVenn: no visible global function definition for
   'plot.new'
mergePlusMinusPeaks: no visible global function definition for
   'read.table'
mergePlusMinusPeaks: no visible global function definition for
   'write.table'
newAnnoGR: no visible global function definition for 'setNames'
oligoSummary : subgroupMotif: no visible global function definition for
   'adist'
oligoSummary : subgroupMotif : : no visible global function
   definition for 'combn'
oligoSummary : subgroupMotif :  : : no visible
   global function definition for 'combn'
oligoSummary: no visible global function definition for 'adist'
oligoSummary: no visible global function 

Re: [Bioc-devel] some new warnings in a package

[Martin Morgan]

On 05/02/2016 12:37 PM, Ludwig Geistlinger wrote:

So yes, you should update the NAMESPACE file following the warning
message you see in your build report.


Hi Martin, I did not encounter such a note on importing from base packages
ever before - but ok, I followed your suggestion and added the imports.


yes, these warnings are relative new.


However all remaining NOTEs and WARNINGs that appeared in the latest build
persist, for example

* checking for code/documentation mismatches ... WARNING

just issues a warning with any further details.


ok thanks for pointing that out.

I believe this is a change in R, but the immediate culprit is 
BiocInstaller (indirectly loaded by AnnotationHub and other dependencies 
of your package). R CMD check would try and capture the 'stderr' stream 
to check for errors. BiocInstaller would try and capture the 'stderr' 
stream on package load to check for https capabilities [primarily a 
left-over from earlier version of R, where a output went directly to 
stderr rather than to a message or warning). BiocInstaller interfered 
with R CMD check.


This is fixed in BiocInstaller 1.21.7.

Thanks for the bug report and your persistence.

Martin




Thx,
Ludwig





On 05/02/2016 11:11 AM, Ludwig Geistlinger wrote:

I encounter the same issue with EnrichmentBrowser - and apparently,
several other packages too, e.g. ensembldb, erma, ExiMiR ...

The warnings seem to be, at first glance, linked to messages e.g. for
masking:

---

* checking S3 generic/method consistency ... WARNING


Attaching package: 'EnrichmentBrowser'

The following object is masked from 'package:BiocGenerics':

  normalize

See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.



However, even when renaming the function, so that masking is not
necessary
(and the message is thus not given anymore), the issue persists.

There seems to be something weird with the current R-devel (2016-04-29
r70565), as R CMD check as prompts me to import from base packages:

-
Undefined global functions or variables:
available.packages browseURL capture.output col2rgb data dev.off
formula head mad median memory.limit model.matrix p.adjust par pchisq
phyper png pnorm qnorm quantile read.delim rgb rnorm runif sd
segments symbols text unzip write.table
Consider adding
importFrom("grDevices", "col2rgb", "dev.off", "png", "rgb")
importFrom("graphics", "par", "segments", "symbols", "text")
importFrom("stats", "formula", "mad", "median", "model.matrix",
   "p.adjust", "pchisq", "phyper", "pnorm", "qnorm",
   "quantile", "rnorm", "runif", "sd")
importFrom("utils", "available.packages", "browseURL",
   "capture.output", "data", "head", "memory.limit",
   "read.delim", "unzip", "write.table")
to your NAMESPACE file.
---


the advice here -- to import from base packages -- is correct. This
ensures that a user cannot define a function, e.g., col2rgb, that masks
the one in grDevices. It is appropriate because these base packages are
not by default imported into your package namespace, so symbols are
resolved by looking on the search() path. The only exception to this is
the actual 'base' package, which _is_ imported by default.

The advice is conservative, in that it does not say that you should add
Imports: grDevices etc to your NAMESPACE file. This is also correct, in
that the grDevices package is always installed.





Martin



Somebody an idea? Or just waiting for the next R-devel snapshot?

Thx,
Ludwig






On Fri, 29-04-2016, at 23:49, Martin Morgan
 wrote:

On 04/29/2016 05:23 PM, Ramon Diaz-Uriarte wrote:

Dear All,

In case it matters, and since we are past the 22, I just noticed that
a
package I maintain (ADaCGH2) is giving warnings in Linux and Mac
(e.g.,
https://www.bioconductor.org/checkResults/devel/bioc-LATEST/ADaCGH2/zin2-checksrc.html)
that, if I recall correctly, were not being given around the 22nd. I
think
these warnings have started appearing with the latest Rs in BioC
(around
r70549?). I haven't been able to understand the ultimate cause of the
warnings (as they seem to refer to issues that are not in the code of
my
package), but they disappear when I move a package from Imports to
Depends.


They seem to come from GLAD's use of packageStartupMessage() in
.onLoad
(e.g., when the package is imported) rather than the recommended
.onAttach (when the package is attached to the search() path, e.g.,
via
library() or Depends: in the DESCRIPTION file).

I updated GLAD to use packageStartuupMessage() in .onAttach; I think
the
warnings will go away.


Martin, thanks for the reply and details. And sorry 

[Bioc-devel] How to debug for the warnings?

[Ou, Jianhong]

Hi All,


I got some warnings when check. However, I could not see any details for that 
warnings. How could I debug for these kind of warnings? Thank you.


* using log directory �/home/biocbuild/bbs-3.3-bioc/meat/ChIPpeakAnno.Rcheck�
* using R version 3.3.0 RC (2016-04-25 r70549)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option �--no-vignettes�
* checking for file �ChIPpeakAnno/DESCRIPTION� ... OK
* checking extension type ... Package
* this is package �ChIPpeakAnno� version �3.5.18�
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  �grid� �IRanges� �Biostrings� �GenomicRanges� �S4Vectors�
  �VennDiagram�
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package �ChIPpeakAnno� can be installed ... [20s/22s] OK
* checking installed package size ... NOTE
  installed size is 19.4Mb
  sub-directories of 1Mb or more:
data 12.7Mb
extdata   5.2Mb
* checking package directory ... OK
* checking �build� directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE

* checking S3 generic/method consistency ... WARNING

See section �Generic functions and methods� in the �Writing R
Extensions� manual.
* checking replacement functions ... WARNING

The argument of a replacement function which corresponds to the right
hand side must be named �value�.
* checking foreign function calls ... NOTE

See chapter �System and foreign language interfaces� in the �Writing R
Extensions� manual.
* checking R code for possible problems ... NOTE
BED2RangedData: no visible global function definition for 'read.delim'
GFF2RangedData: no visible global function definition for 'read.delim'
addGeneIDs : is.installed: no visible global function definition for
  'installed.packages'
binOverFeature: no visible global function definition for 'par'
binOverFeature : plotErrBar: no visible global function definition for
  'segments'
binOverFeature : plotErrBar: no visible global function definition for
  'par'
binOverFeature : : no visible global function definition for
  'plot'
binOverFeature : : no visible global function definition for
  'abline'
binOverFeature : : no visible global function definition for
  'axis'
buildBindingDistribution: no visible global function definition for
  'boxplot.stats'
buildBindingDistribution: no visible global function definition for
  'hist'
df2GRanges : : no visible global function definition for
  'rgb'
egOrgMap: no visible global function definition for 'adist'
featureAlignedDistribution: no visible global function definition for
  'matplot'
featureAlignedDistribution: no visible global function definition for
  'axis'
featureAlignedDistribution: no visible global function definition for
  'legend'
featureAlignedHeatmap: no visible global function definition for
  'colorRampPalette'
featureAlignedHeatmap : areColors : : no visible global
  function definition for 'col2rgb'
findOverlappingPeaks : : no visible binding for global
  variable 'data'
makeVennDiagram : plotVenn: no visible global function definition for
  'par'
makeVennDiagram : plotVenn: no visible global function definition for
  'plot.new'
mergePlusMinusPeaks: no visible global function definition for
  'read.table'
mergePlusMinusPeaks: no visible global function definition for
  'write.table'
newAnnoGR: no visible global function definition for 'setNames'
oligoSummary : subgroupMotif: no visible global function definition for
  'adist'
oligoSummary : subgroupMotif : : no visible global function
  definition for 'combn'
oligoSummary : subgroupMotif :  : : no visible
  global function definition for 'combn'
oligoSummary: no visible global function definition for 'adist'
oligoSummary: no visible global function definition for 'hclust'
oligoSummary: no visible global function definition for 'kmeans'
oligoSummary: no visible global function definition for 'as.dendrogram'
oligoSummary: no visible binding for global variable 'nobs'
pie1: no visible global function definition for 'as.graphicsAnnot'

Re: [Bioc-devel] select(Homo.sapiens,...) failing

[Obenchain, Valerie]

Hi Vince,

You need version >=1.13.9 of OrganismDbi. Unfortunately it's failing
check because of the biomart problems so you'll have to get it from svn.
Let me know if you still have problems after updating.

Val


On 05/02/2016 11:53 AM, Vincent Carey wrote:
> biocValid() says all is well ...
>
>> select(Homo.sapiens, keys="1001", keytype="ENTREZID", columns="SYMBOL")
> *Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : *
>
> *  object '.testSelectArgs' not found*
>
>> sessionInfo()
> R version 3.3.0 beta (2016-04-01 r70412)
>
> Platform: x86_64-apple-darwin13.4.0 (64-bit)
>
> Running under: OS X 10.10.5 (Yosemite)
>
>
> locale:
>
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
>
> attached base packages:
>
> [1] parallel  stats4stats graphics  grDevices utils datasets
>
> [8] methods   base
>
>
> other attached packages:
>
>  [1] Homo.sapiens_1.3.1
>
>  [2] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
>
>  [3] org.Hs.eg.db_3.3.0
>
>  [4] GO.db_3.3.0
>
>  [5] OrganismDbi_1.13.8
>
>  [6] GenomicFeatures_1.23.31
>
>  [7] GenomicRanges_1.23.27
>
>  [8] GenomeInfoDb_1.7.6
>
>  [9] AnnotationDbi_1.33.15
>
> [10] IRanges_2.5.46
>
>
> [11] S4Vectors_0.9.52
>
> [12] Biobase_2.31.3
>
> [13] BiocGenerics_0.17.5
>
> [14] BiocInstaller_1.21.6
>
>
> loaded via a namespace (and not attached):
>
>  [1] graph_1.49.1Rcpp_0.12.4.5
>
>  [3] XVector_0.11.8  zlibbioc_1.17.1
>
>  [5] GenomicAlignments_1.7.21BiocParallel_1.5.22
>
>  [7] tools_3.3.0 SummarizedExperiment_1.1.27
>
>  [9] DBI_0.4 RBGL_1.47.0
>
> [11] rtracklayer_1.31.11 bitops_1.0-6
>
> [13] RCurl_1.95-4.8  biomaRt_2.27.2
>
> [15] RSQLite_1.0.0   Biostrings_2.39.14
>
> [17] Rsamtools_1.23.11   XML_3.98-1.4
>
>   [[alternative HTML version deleted]]
>
> ___
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>



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Re: [Bioc-devel] could not install S4Vectors in Mac OS 10.8.5

[Dan Tenenbaum]

Well, you can tell your helpdesk that this is going to impact people's work as 
the OS you are using will no longer be supported by R/Bioconductor starting 
with the release this week.

Mavericks was released 3 years ago. It seems reasonable to support it now.

Dan


- Original Message -
> From: "Jianhong Ou" 
> To: "Dan Tenenbaum" 
> Cc: "bioc-devel" 
> Sent: Monday, May 2, 2016 12:34:47 PM
> Subject: Re: [Bioc-devel] could not install S4Vectors in Mac OS 10.8.5

> Hi Dan,
> 
> Thank you for your answer. I hope I can update to Mavericks but our help
> desk just ask me to hold on current OS.
> 
> Yours Sincerely,
> 
> Jianhong Ou
> 
> TEL: 508-856-5379
> LRB 608
> Bioinformatician of Bioinformatics core at
> Department of Molecular, Cell and Cancer Biology
> 364 Plantation Street Worcester,
> MA 01605
> 
> 
> 
> 
> On 5/2/16 3:04 PM, "Dan Tenenbaum"  wrote:
> 
>>This question should probably go on the support site as it is not about
>>package development.
>>
>>You should update to Mavericks or higher. Earlier versions of Mac OS X
>>are no longer officially supported by R or Bioconductor (that's why a
>>binary is not available).
>>
>>
>>Dan
>>
>>
>>- Original Message -
>>> From: "Jianhong Ou" 
>>> To: "bioc-devel" 
>>> Sent: Monday, May 2, 2016 12:00:09 PM
>>> Subject: [Bioc-devel] could not install S4Vectors in Mac OS 10.8.5
>>
>>> Hi,
>>> 
>>> I got error when I update S4Vectors in R 3.3 RC r70564 today. I also
>>>tried
>>> r70549, same error like this
>>> 
 biocLite()
>>> BioC_mirror: https://bioconductor.org
>>> Using Bioconductor 3.3 (BiocInstaller 1.21.6), R 3.3.0 RC (2016-04-28
>>>r70564).
>>> Old packages: 'S4Vectors'
>>> Update all/some/none? [a/s/n]:
>>> a
>>> trying URL
>>> 
>>>'https://bioconductor.org/packages/3.3/bioc/src/contrib/S4Vectors_0.9.52.
>>>tar.gz'
>>> Content type 'application/x-gzip' length 225431 bytes (220 KB)
>>> ==
>>> downloaded 220 KB
>>> 
>>> * installing *source* package �S4Vectors� ...
>>> ** libs
>>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>> -I/usr/local/include-fPIC  -g -O2  -c AEbufs.c -o AEbufs.o
>>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>> -I/usr/local/include-fPIC  -g -O2  -c DataFrame_class.c -o
>>> DataFrame_class.o
>>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>> -I/usr/local/include-fPIC  -g -O2  -c Hits_class.c -o Hits_class.o
>>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>> -I/usr/local/include-fPIC  -g -O2  -c List_class.c -o List_class.o
>>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>> -I/usr/local/include-fPIC  -g -O2  -c R_init_S4Vectors.c -o
>>> R_init_S4Vectors.o
>>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>> -I/usr/local/include-fPIC  -g -O2  -c Rle_class.c -o Rle_class.o
>>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>> -I/usr/local/include-fPIC  -g -O2  -c Rle_utils.c -o Rle_utils.o
>>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>> -I/usr/local/include-fPIC  -g -O2  -c SEXP_utils.c -o SEXP_utils.o
>>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>> -I/usr/local/include-fPIC  -g -O2  -c SimpleList_class.c -o
>>> SimpleList_class.o
>>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>> -I/usr/local/include-fPIC  -g -O2  -c anyMissing.c -o anyMissing.o
>>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>> -I/usr/local/include-fPIC  -g -O2  -c eval_utils.c -o eval_utils.o
>>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>> -I/usr/local/include-fPIC  -g -O2  -c hash_utils.c -o hash_utils.o
>>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>> -I/usr/local/include-fPIC  -g -O2  -c int_utils.c -o int_utils.o
>>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>> -I/usr/local/include-fPIC  -g -O2  -c logical_utils.c -o
>>>logical_utils.o
>>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>> -I/usr/local/include-fPIC  -g -O2  -c safe_arithm.c -o safe_arithm.o
>>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>> -I/usr/local/include-fPIC  -g -O2  -c sort_utils.c -o sort_utils.o
>>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>> -I/usr/local/include-fPIC  -g -O2  -c str_utils.c -o str_utils.o
>>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>> -I/usr/local/include-fPIC  -g -O2  -c vector_utils.c -o
>>>vector_utils.o
>>> gcc -dynamiclib -Wl,-headerpad_max_install_names -undefined
>>>dynamic_lookup
>>> -single_module -multiply_defined suppress
>>> 

Re: [Bioc-devel] could not install S4Vectors in Mac OS 10.8.5

[Ou, Jianhong]

Hi Dan,

Thank you for your answer. I hope I can update to Mavericks but our help
desk just ask me to hold on current OS.

Yours Sincerely,

Jianhong Ou

TEL: 508-856-5379
LRB 608
Bioinformatician of Bioinformatics core at
Department of Molecular, Cell and Cancer Biology
364 Plantation Street Worcester,
MA 01605




On 5/2/16 3:04 PM, "Dan Tenenbaum"  wrote:

>This question should probably go on the support site as it is not about
>package development.
>
>You should update to Mavericks or higher. Earlier versions of Mac OS X
>are no longer officially supported by R or Bioconductor (that's why a
>binary is not available).
>
>
>Dan
>
>
>- Original Message -
>> From: "Jianhong Ou" 
>> To: "bioc-devel" 
>> Sent: Monday, May 2, 2016 12:00:09 PM
>> Subject: [Bioc-devel] could not install S4Vectors in Mac OS 10.8.5
>
>> Hi,
>> 
>> I got error when I update S4Vectors in R 3.3 RC r70564 today. I also
>>tried
>> r70549, same error like this
>> 
>>> biocLite()
>> BioC_mirror: https://bioconductor.org
>> Using Bioconductor 3.3 (BiocInstaller 1.21.6), R 3.3.0 RC (2016-04-28
>>r70564).
>> Old packages: 'S4Vectors'
>> Update all/some/none? [a/s/n]:
>> a
>> trying URL
>> 
>>'https://bioconductor.org/packages/3.3/bioc/src/contrib/S4Vectors_0.9.52.
>>tar.gz'
>> Content type 'application/x-gzip' length 225431 bytes (220 KB)
>> ==
>> downloaded 220 KB
>> 
>> * installing *source* package �S4Vectors� ...
>> ** libs
>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>> -I/usr/local/include-fPIC  -g -O2  -c AEbufs.c -o AEbufs.o
>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>> -I/usr/local/include-fPIC  -g -O2  -c DataFrame_class.c -o
>> DataFrame_class.o
>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>> -I/usr/local/include-fPIC  -g -O2  -c Hits_class.c -o Hits_class.o
>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>> -I/usr/local/include-fPIC  -g -O2  -c List_class.c -o List_class.o
>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>> -I/usr/local/include-fPIC  -g -O2  -c R_init_S4Vectors.c -o
>> R_init_S4Vectors.o
>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>> -I/usr/local/include-fPIC  -g -O2  -c Rle_class.c -o Rle_class.o
>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>> -I/usr/local/include-fPIC  -g -O2  -c Rle_utils.c -o Rle_utils.o
>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>> -I/usr/local/include-fPIC  -g -O2  -c SEXP_utils.c -o SEXP_utils.o
>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>> -I/usr/local/include-fPIC  -g -O2  -c SimpleList_class.c -o
>> SimpleList_class.o
>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>> -I/usr/local/include-fPIC  -g -O2  -c anyMissing.c -o anyMissing.o
>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>> -I/usr/local/include-fPIC  -g -O2  -c eval_utils.c -o eval_utils.o
>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>> -I/usr/local/include-fPIC  -g -O2  -c hash_utils.c -o hash_utils.o
>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>> -I/usr/local/include-fPIC  -g -O2  -c int_utils.c -o int_utils.o
>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>> -I/usr/local/include-fPIC  -g -O2  -c logical_utils.c -o
>>logical_utils.o
>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>> -I/usr/local/include-fPIC  -g -O2  -c safe_arithm.c -o safe_arithm.o
>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>> -I/usr/local/include-fPIC  -g -O2  -c sort_utils.c -o sort_utils.o
>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>> -I/usr/local/include-fPIC  -g -O2  -c str_utils.c -o str_utils.o
>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>> -I/usr/local/include-fPIC  -g -O2  -c vector_utils.c -o
>>vector_utils.o
>> gcc -dynamiclib -Wl,-headerpad_max_install_names -undefined
>>dynamic_lookup
>> -single_module -multiply_defined suppress
>> -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o
>> S4Vectors.so AEbufs.o DataFrame_class.o Hits_class.o List_class.o
>> R_init_S4Vectors.o Rle_class.o Rle_utils.o SEXP_utils.o
>>SimpleList_class.o
>> anyMissing.o eval_utils.o hash_utils.o int_utils.o logical_utils.o
>> safe_arithm.o sort_utils.o str_utils.o vector_utils.o
>> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
>> -Wl,CoreFoundation
>> installing to
>> 
>>/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/
>>libs
>> ** R
>> ** inst
>> ** preparing package for lazy loading
>> Creating a generic function for �head� from package �utils� in package
>> �S4Vectors�
>> Creating a generic function for 

Re: [Bioc-devel] could not install S4Vectors in Mac OS 10.8.5

[Ou, Jianhong]

Dear Herve,

After reinstalling BiocGenerics, there is no errors any more. Thank you
very much. 

Yours Sincerely,

Jianhong Ou

TEL: 508-856-5379
LRB 608
Bioinformatician of Bioinformatics core at
Department of Molecular, Cell and Cancer Biology
364 Plantation Street Worcester,
MA 01605




On 5/2/16 3:15 PM, "Hervé Pagès"  wrote:

>Hi Jianhong,
>
>order() got a new argument in R 3.3 and the order() generic in
>BiocGenerics was modified accordingly. Please try to re-install
>BiocGenerics before you try to update S4Vectors. In fact, when
>updating R, all your packages should be re-installed. Most people
>don't do it because that takes a long time but there is no guarantee
>that packages installed under a previous version of R will still work
>properly with a new version of R.
>
>H.
>
>On 05/02/2016 12:00 PM, Ou, Jianhong wrote:
>> Hi,
>>
>> I got error when I update S4Vectors in R 3.3 RC r70564 today. I also
>>tried r70549, same error like this
>>
>>> biocLite()
>> BioC_mirror: https://bioconductor.org
>> Using Bioconductor 3.3 (BiocInstaller 1.21.6), R 3.3.0 RC (2016-04-28
>>r70564).
>> Old packages: 'S4Vectors'
>> Update all/some/none? [a/s/n]:
>> a
>> trying URL 
>>'https://bioconductor.org/packages/3.3/bioc/src/contrib/S4Vectors_0.9.52.
>>tar.gz'
>> Content type 'application/x-gzip' length 225431 bytes (220 KB)
>> ==
>> downloaded 220 KB
>>
>> * installing *source* package �S4Vectors� ...
>> ** libs
>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>-I/usr/local/include-fPIC  -g -O2  -c AEbufs.c -o AEbufs.o
>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>-I/usr/local/include-fPIC  -g -O2  -c DataFrame_class.c -o
>>DataFrame_class.o
>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>-I/usr/local/include-fPIC  -g -O2  -c Hits_class.c -o Hits_class.o
>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>-I/usr/local/include-fPIC  -g -O2  -c List_class.c -o List_class.o
>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>-I/usr/local/include-fPIC  -g -O2  -c R_init_S4Vectors.c -o
>>R_init_S4Vectors.o
>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>-I/usr/local/include-fPIC  -g -O2  -c Rle_class.c -o Rle_class.o
>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>-I/usr/local/include-fPIC  -g -O2  -c Rle_utils.c -o Rle_utils.o
>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>-I/usr/local/include-fPIC  -g -O2  -c SEXP_utils.c -o SEXP_utils.o
>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>-I/usr/local/include-fPIC  -g -O2  -c SimpleList_class.c -o
>>SimpleList_class.o
>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>-I/usr/local/include-fPIC  -g -O2  -c anyMissing.c -o anyMissing.o
>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>-I/usr/local/include-fPIC  -g -O2  -c eval_utils.c -o eval_utils.o
>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>-I/usr/local/include-fPIC  -g -O2  -c hash_utils.c -o hash_utils.o
>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>-I/usr/local/include-fPIC  -g -O2  -c int_utils.c -o int_utils.o
>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>-I/usr/local/include-fPIC  -g -O2  -c logical_utils.c -o
>>logical_utils.o
>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>-I/usr/local/include-fPIC  -g -O2  -c safe_arithm.c -o safe_arithm.o
>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>-I/usr/local/include-fPIC  -g -O2  -c sort_utils.c -o sort_utils.o
>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>-I/usr/local/include-fPIC  -g -O2  -c str_utils.c -o str_utils.o
>> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
>>-I/usr/local/include-fPIC  -g -O2  -c vector_utils.c -o
>>vector_utils.o
>> gcc -dynamiclib -Wl,-headerpad_max_install_names -undefined
>>dynamic_lookup -single_module -multiply_defined suppress
>>-L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o
>>S4Vectors.so AEbufs.o DataFrame_class.o Hits_class.o List_class.o
>>R_init_S4Vectors.o Rle_class.o Rle_utils.o SEXP_utils.o
>>SimpleList_class.o anyMissing.o eval_utils.o hash_utils.o int_utils.o
>>logical_utils.o safe_arithm.o sort_utils.o str_utils.o vector_utils.o
>>-F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
>>-Wl,CoreFoundation
>> installing to 
>>/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/
>>libs
>> ** R
>> ** inst
>> ** preparing package for lazy loading
>> Creating a generic function for �head� from package �utils� in package
>>�S4Vectors�
>> Creating a generic function for �tail� from package �utils� in package
>>�S4Vectors�
>> Creating a generic function for 

[Bioc-devel] could not install S4Vectors in Mac OS 10.8.5

[Ou, Jianhong]

Hi,

I got error when I update S4Vectors in R 3.3 RC r70564 today. I also tried 
r70549, same error like this

> biocLite()
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.21.6), R 3.3.0 RC (2016-04-28 r70564).
Old packages: 'S4Vectors'
Update all/some/none? [a/s/n]:
a
trying URL 
'https://bioconductor.org/packages/3.3/bioc/src/contrib/S4Vectors_0.9.52.tar.gz'
Content type 'application/x-gzip' length 225431 bytes (220 KB)
==
downloaded 220 KB

* installing *source* package �S4Vectors� ...
** libs
gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  
-I/usr/local/include-fPIC  -g -O2  -c AEbufs.c -o AEbufs.o
gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  
-I/usr/local/include-fPIC  -g -O2  -c DataFrame_class.c -o DataFrame_class.o
gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  
-I/usr/local/include-fPIC  -g -O2  -c Hits_class.c -o Hits_class.o
gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  
-I/usr/local/include-fPIC  -g -O2  -c List_class.c -o List_class.o
gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  
-I/usr/local/include-fPIC  -g -O2  -c R_init_S4Vectors.c -o 
R_init_S4Vectors.o
gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  
-I/usr/local/include-fPIC  -g -O2  -c Rle_class.c -o Rle_class.o
gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  
-I/usr/local/include-fPIC  -g -O2  -c Rle_utils.c -o Rle_utils.o
gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  
-I/usr/local/include-fPIC  -g -O2  -c SEXP_utils.c -o SEXP_utils.o
gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  
-I/usr/local/include-fPIC  -g -O2  -c SimpleList_class.c -o 
SimpleList_class.o
gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  
-I/usr/local/include-fPIC  -g -O2  -c anyMissing.c -o anyMissing.o
gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  
-I/usr/local/include-fPIC  -g -O2  -c eval_utils.c -o eval_utils.o
gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  
-I/usr/local/include-fPIC  -g -O2  -c hash_utils.c -o hash_utils.o
gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  
-I/usr/local/include-fPIC  -g -O2  -c int_utils.c -o int_utils.o
gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  
-I/usr/local/include-fPIC  -g -O2  -c logical_utils.c -o logical_utils.o
gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  
-I/usr/local/include-fPIC  -g -O2  -c safe_arithm.c -o safe_arithm.o
gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  
-I/usr/local/include-fPIC  -g -O2  -c sort_utils.c -o sort_utils.o
gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  
-I/usr/local/include-fPIC  -g -O2  -c str_utils.c -o str_utils.o
gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  
-I/usr/local/include-fPIC  -g -O2  -c vector_utils.c -o vector_utils.o
gcc -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup 
-single_module -multiply_defined suppress 
-L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o 
S4Vectors.so AEbufs.o DataFrame_class.o Hits_class.o List_class.o 
R_init_S4Vectors.o Rle_class.o Rle_utils.o SEXP_utils.o SimpleList_class.o 
anyMissing.o eval_utils.o hash_utils.o int_utils.o logical_utils.o 
safe_arithm.o sort_utils.o str_utils.o vector_utils.o 
-F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework 
-Wl,CoreFoundation
installing to 
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for �head� from package �utils� in package 
�S4Vectors�
Creating a generic function for �tail� from package �utils� in package 
�S4Vectors�
Creating a generic function for �na.omit� from package �stats� in package 
�S4Vectors�
Creating a generic function for �na.exclude� from package �stats� in package 
�S4Vectors�
Creating a generic function for �complete.cases� from package �stats� in 
package �S4Vectors�
Creating a generic function for �transform� from package �base� in package 
�S4Vectors�
Creating a generic function for �merge� from package �base� in package 
�S4Vectors�
Creating a new generic function for �rowSums� in package �S4Vectors�
Creating a new generic function for �colSums� in package �S4Vectors�
Creating a new generic function for �rowMeans� in package �S4Vectors�
Creating a new generic function for �colMeans� in package �S4Vectors�
Creating a generic function for �as.matrix� from package �base� in package 
�S4Vectors�
Creating a generic function for �window� from package �stats� in package 
�S4Vectors�
Creating a generic function for �with� from package �base� in package 
�S4Vectors�
Creating a new generic function for �expand.grid� in package �S4Vectors�

Re: [Bioc-devel] could not install S4Vectors in Mac OS 10.8.5

[Dan Tenenbaum]

This question should probably go on the support site as it is not about package 
development.

You should update to Mavericks or higher. Earlier versions of Mac OS X are no 
longer officially supported by R or Bioconductor (that's why a binary is not 
available).


Dan


- Original Message -
> From: "Jianhong Ou" 
> To: "bioc-devel" 
> Sent: Monday, May 2, 2016 12:00:09 PM
> Subject: [Bioc-devel] could not install S4Vectors in Mac OS 10.8.5

> Hi,
> 
> I got error when I update S4Vectors in R 3.3 RC r70564 today. I also tried
> r70549, same error like this
> 
>> biocLite()
> BioC_mirror: https://bioconductor.org
> Using Bioconductor 3.3 (BiocInstaller 1.21.6), R 3.3.0 RC (2016-04-28 r70564).
> Old packages: 'S4Vectors'
> Update all/some/none? [a/s/n]:
> a
> trying URL
> 'https://bioconductor.org/packages/3.3/bioc/src/contrib/S4Vectors_0.9.52.tar.gz'
> Content type 'application/x-gzip' length 225431 bytes (220 KB)
> ==
> downloaded 220 KB
> 
> * installing *source* package �S4Vectors� ...
> ** libs
> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include-fPIC  -g -O2  -c AEbufs.c -o AEbufs.o
> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include-fPIC  -g -O2  -c DataFrame_class.c -o
> DataFrame_class.o
> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include-fPIC  -g -O2  -c Hits_class.c -o Hits_class.o
> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include-fPIC  -g -O2  -c List_class.c -o List_class.o
> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include-fPIC  -g -O2  -c R_init_S4Vectors.c -o
> R_init_S4Vectors.o
> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include-fPIC  -g -O2  -c Rle_class.c -o Rle_class.o
> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include-fPIC  -g -O2  -c Rle_utils.c -o Rle_utils.o
> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include-fPIC  -g -O2  -c SEXP_utils.c -o SEXP_utils.o
> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include-fPIC  -g -O2  -c SimpleList_class.c -o
> SimpleList_class.o
> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include-fPIC  -g -O2  -c anyMissing.c -o anyMissing.o
> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include-fPIC  -g -O2  -c eval_utils.c -o eval_utils.o
> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include-fPIC  -g -O2  -c hash_utils.c -o hash_utils.o
> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include-fPIC  -g -O2  -c int_utils.c -o int_utils.o
> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include-fPIC  -g -O2  -c logical_utils.c -o logical_utils.o
> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include-fPIC  -g -O2  -c safe_arithm.c -o safe_arithm.o
> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include-fPIC  -g -O2  -c sort_utils.c -o sort_utils.o
> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include-fPIC  -g -O2  -c str_utils.c -o str_utils.o
> gcc -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include-fPIC  -g -O2  -c vector_utils.c -o vector_utils.o
> gcc -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup
> -single_module -multiply_defined suppress
> -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o
> S4Vectors.so AEbufs.o DataFrame_class.o Hits_class.o List_class.o
> R_init_S4Vectors.o Rle_class.o Rle_utils.o SEXP_utils.o SimpleList_class.o
> anyMissing.o eval_utils.o hash_utils.o int_utils.o logical_utils.o
> safe_arithm.o sort_utils.o str_utils.o vector_utils.o
> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
> -Wl,CoreFoundation
> installing to
> /Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/libs
> ** R
> ** inst
> ** preparing package for lazy loading
> Creating a generic function for �head� from package �utils� in package
> �S4Vectors�
> Creating a generic function for �tail� from package �utils� in package
> �S4Vectors�
> Creating a generic function for �na.omit� from package �stats� in package
> �S4Vectors�
> Creating a generic function for �na.exclude� from package �stats� in package
> �S4Vectors�
> Creating a generic function for �complete.cases� from package �stats� in 
> package
> �S4Vectors�
> Creating a generic function for �transform� from package �base� in package
> �S4Vectors�
> Creating a generic function for �merge� from package �base� in 

[Bioc-devel] select(Homo.sapiens,...) failing

[Vincent Carey]

biocValid() says all is well ...

> select(Homo.sapiens, keys="1001", keytype="ENTREZID", columns="SYMBOL")

*Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : *

*  object '.testSelectArgs' not found*

> sessionInfo()

R version 3.3.0 beta (2016-04-01 r70412)

Platform: x86_64-apple-darwin13.4.0 (64-bit)

Running under: OS X 10.10.5 (Yosemite)


locale:

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8


attached base packages:

[1] parallel  stats4stats graphics  grDevices utils datasets

[8] methods   base


other attached packages:

 [1] Homo.sapiens_1.3.1

 [2] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2

 [3] org.Hs.eg.db_3.3.0

 [4] GO.db_3.3.0

 [5] OrganismDbi_1.13.8

 [6] GenomicFeatures_1.23.31

 [7] GenomicRanges_1.23.27

 [8] GenomeInfoDb_1.7.6

 [9] AnnotationDbi_1.33.15

[10] IRanges_2.5.46


[11] S4Vectors_0.9.52

[12] Biobase_2.31.3

[13] BiocGenerics_0.17.5

[14] BiocInstaller_1.21.6


loaded via a namespace (and not attached):

 [1] graph_1.49.1Rcpp_0.12.4.5

 [3] XVector_0.11.8  zlibbioc_1.17.1

 [5] GenomicAlignments_1.7.21BiocParallel_1.5.22

 [7] tools_3.3.0 SummarizedExperiment_1.1.27

 [9] DBI_0.4 RBGL_1.47.0

[11] rtracklayer_1.31.11 bitops_1.0-6

[13] RCurl_1.95-4.8  biomaRt_2.27.2

[15] RSQLite_1.0.0   Biostrings_2.39.14

[17] Rsamtools_1.23.11   XML_3.98-1.4

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Re: [Bioc-devel] some new warnings in a package

[Ludwig Geistlinger]

> So yes, you should update the NAMESPACE file following the warning
> message you see in your build report.

Hi Martin, I did not encounter such a note on importing from base packages
ever before - but ok, I followed your suggestion and added the imports.
However all remaining NOTEs and WARNINGs that appeared in the latest build
persist, for example

* checking for code/documentation mismatches ... WARNING

just issues a warning with any further details.

Thx,
Ludwig


>
>
> On 05/02/2016 11:11 AM, Ludwig Geistlinger wrote:
>> I encounter the same issue with EnrichmentBrowser - and apparently,
>> several other packages too, e.g. ensembldb, erma, ExiMiR ...
>>
>> The warnings seem to be, at first glance, linked to messages e.g. for
>> masking:
>>
>> ---
>>
>> * checking S3 generic/method consistency ... WARNING
>>
>>
>> Attaching package: 'EnrichmentBrowser'
>>
>> The following object is masked from 'package:BiocGenerics':
>>
>>  normalize
>>
>> See section 'Generic functions and methods' in the 'Writing R
>> Extensions' manual.
>>
>> 
>>
>> However, even when renaming the function, so that masking is not
>> necessary
>> (and the message is thus not given anymore), the issue persists.
>>
>> There seems to be something weird with the current R-devel (2016-04-29
>> r70565), as R CMD check as prompts me to import from base packages:
>>
>> -
>> Undefined global functions or variables:
>>available.packages browseURL capture.output col2rgb data dev.off
>>formula head mad median memory.limit model.matrix p.adjust par pchisq
>>phyper png pnorm qnorm quantile read.delim rgb rnorm runif sd
>>segments symbols text unzip write.table
>> Consider adding
>>importFrom("grDevices", "col2rgb", "dev.off", "png", "rgb")
>>importFrom("graphics", "par", "segments", "symbols", "text")
>>importFrom("stats", "formula", "mad", "median", "model.matrix",
>>   "p.adjust", "pchisq", "phyper", "pnorm", "qnorm",
>>   "quantile", "rnorm", "runif", "sd")
>>importFrom("utils", "available.packages", "browseURL",
>>   "capture.output", "data", "head", "memory.limit",
>>   "read.delim", "unzip", "write.table")
>> to your NAMESPACE file.
>> ---
>
> the advice here -- to import from base packages -- is correct. This
> ensures that a user cannot define a function, e.g., col2rgb, that masks
> the one in grDevices. It is appropriate because these base packages are
> not by default imported into your package namespace, so symbols are
> resolved by looking on the search() path. The only exception to this is
> the actual 'base' package, which _is_ imported by default.
>
> The advice is conservative, in that it does not say that you should add
> Imports: grDevices etc to your NAMESPACE file. This is also correct, in
> that the grDevices package is always installed.
>

>
> Martin
>
>>
>> Somebody an idea? Or just waiting for the next R-devel snapshot?
>>
>> Thx,
>> Ludwig
>>
>>
>>>
>>>
>>>
>>> On Fri, 29-04-2016, at 23:49, Martin Morgan
>>>  wrote:
 On 04/29/2016 05:23 PM, Ramon Diaz-Uriarte wrote:
> Dear All,
>
> In case it matters, and since we are past the 22, I just noticed that
> a
> package I maintain (ADaCGH2) is giving warnings in Linux and Mac
> (e.g.,
> https://www.bioconductor.org/checkResults/devel/bioc-LATEST/ADaCGH2/zin2-checksrc.html)
> that, if I recall correctly, were not being given around the 22nd. I
> think
> these warnings have started appearing with the latest Rs in BioC
> (around
> r70549?). I haven't been able to understand the ultimate cause of the
> warnings (as they seem to refer to issues that are not in the code of
> my
> package), but they disappear when I move a package from Imports to
> Depends.

 They seem to come from GLAD's use of packageStartupMessage() in
 .onLoad
 (e.g., when the package is imported) rather than the recommended
 .onAttach (when the package is attached to the search() path, e.g.,
 via
 library() or Depends: in the DESCRIPTION file).

 I updated GLAD to use packageStartuupMessage() in .onAttach; I think
 the
 warnings will go away.
>>>
>>> Martin, thanks for the reply and details. And sorry for my
>>> not-particularly-explicit message; yes, GLAD is the package that I
>>> moved
>>> to
>>> Depends. And I did not say (though I had intended too ---time to go to
>>> bed)
>>> that I had committed my changes to svn.
>>>
>>> Anyway, should I revert my changes to keep GLAD in Imports?
>>>
>>> Best,
>>>
>>> R.
>>>
>>>

 Martin

>
>
> Best,
>
> R.
>
>
>
>

Re: [Bioc-devel] some new warnings in a package

[Martin Morgan]

On 05/02/2016 11:11 AM, Ludwig Geistlinger wrote:

I encounter the same issue with EnrichmentBrowser - and apparently,
several other packages too, e.g. ensembldb, erma, ExiMiR ...

The warnings seem to be, at first glance, linked to messages e.g. for
masking:

---

* checking S3 generic/method consistency ... WARNING


Attaching package: 'EnrichmentBrowser'

The following object is masked from 'package:BiocGenerics':

 normalize

See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.



However, even when renaming the function, so that masking is not necessary
(and the message is thus not given anymore), the issue persists.

There seems to be something weird with the current R-devel (2016-04-29
r70565), as R CMD check as prompts me to import from base packages:

-
Undefined global functions or variables:
   available.packages browseURL capture.output col2rgb data dev.off
   formula head mad median memory.limit model.matrix p.adjust par pchisq
   phyper png pnorm qnorm quantile read.delim rgb rnorm runif sd
   segments symbols text unzip write.table
Consider adding
   importFrom("grDevices", "col2rgb", "dev.off", "png", "rgb")
   importFrom("graphics", "par", "segments", "symbols", "text")
   importFrom("stats", "formula", "mad", "median", "model.matrix",
  "p.adjust", "pchisq", "phyper", "pnorm", "qnorm",
  "quantile", "rnorm", "runif", "sd")
   importFrom("utils", "available.packages", "browseURL",
  "capture.output", "data", "head", "memory.limit",
  "read.delim", "unzip", "write.table")
to your NAMESPACE file.
---


the advice here -- to import from base packages -- is correct. This 
ensures that a user cannot define a function, e.g., col2rgb, that masks 
the one in grDevices. It is appropriate because these base packages are 
not by default imported into your package namespace, so symbols are 
resolved by looking on the search() path. The only exception to this is 
the actual 'base' package, which _is_ imported by default.


The advice is conservative, in that it does not say that you should add 
Imports: grDevices etc to your NAMESPACE file. This is also correct, in 
that the grDevices package is always installed.


So yes, you should update the NAMESPACE file following the warning 
message you see in your build report.


Martin



Somebody an idea? Or just waiting for the next R-devel snapshot?

Thx,
Ludwig






On Fri, 29-04-2016, at 23:49, Martin Morgan
 wrote:

On 04/29/2016 05:23 PM, Ramon Diaz-Uriarte wrote:

Dear All,

In case it matters, and since we are past the 22, I just noticed that a
package I maintain (ADaCGH2) is giving warnings in Linux and Mac (e.g.,
https://www.bioconductor.org/checkResults/devel/bioc-LATEST/ADaCGH2/zin2-checksrc.html)
that, if I recall correctly, were not being given around the 22nd. I
think
these warnings have started appearing with the latest Rs in BioC
(around
r70549?). I haven't been able to understand the ultimate cause of the
warnings (as they seem to refer to issues that are not in the code of
my
package), but they disappear when I move a package from Imports to
Depends.


They seem to come from GLAD's use of packageStartupMessage() in .onLoad
(e.g., when the package is imported) rather than the recommended
.onAttach (when the package is attached to the search() path, e.g., via
library() or Depends: in the DESCRIPTION file).

I updated GLAD to use packageStartuupMessage() in .onAttach; I think the
warnings will go away.


Martin, thanks for the reply and details. And sorry for my
not-particularly-explicit message; yes, GLAD is the package that I moved
to
Depends. And I did not say (though I had intended too ---time to go to
bed)
that I had committed my changes to svn.

Anyway, should I revert my changes to keep GLAD in Imports?

Best,

R.




Martin




Best,

R.







This email message may contain legally privileged and/or confidential
information.  If you are not the intended recipient(s), or the employee
or agent responsible for the delivery of this message to the intended
recipient(s), you are hereby notified that any disclosure, copying,
distribution, or use of this email message is prohibited.  If you have
received this message in error, please notify the sender immediately by
e-mail and delete this email message from your computer. Thank you.



--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain

Phone: +34-91-497-2412

Email: rdia...@gmail.com
ramon.d...@iib.uam.es

http://ligarto.org/rdiaz

___

Re: [Bioc-devel] some new warnings in a package

[Ludwig Geistlinger]

I encounter the same issue with EnrichmentBrowser - and apparently,
several other packages too, e.g. ensembldb, erma, ExiMiR ...

The warnings seem to be, at first glance, linked to messages e.g. for
masking:

---

* checking S3 generic/method consistency ... WARNING


Attaching package: 'EnrichmentBrowser'

The following object is masked from 'package:BiocGenerics':

normalize

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.



However, even when renaming the function, so that masking is not necessary
(and the message is thus not given anymore), the issue persists.

There seems to be something weird with the current R-devel (2016-04-29
r70565), as R CMD check as prompts me to import from base packages:

-
Undefined global functions or variables:
  available.packages browseURL capture.output col2rgb data dev.off
  formula head mad median memory.limit model.matrix p.adjust par pchisq
  phyper png pnorm qnorm quantile read.delim rgb rnorm runif sd
  segments symbols text unzip write.table
Consider adding
  importFrom("grDevices", "col2rgb", "dev.off", "png", "rgb")
  importFrom("graphics", "par", "segments", "symbols", "text")
  importFrom("stats", "formula", "mad", "median", "model.matrix",
 "p.adjust", "pchisq", "phyper", "pnorm", "qnorm",
 "quantile", "rnorm", "runif", "sd")
  importFrom("utils", "available.packages", "browseURL",
 "capture.output", "data", "head", "memory.limit",
 "read.delim", "unzip", "write.table")
to your NAMESPACE file.
---

Somebody an idea? Or just waiting for the next R-devel snapshot?

Thx,
Ludwig


>
>
>
> On Fri, 29-04-2016, at 23:49, Martin Morgan
>  wrote:
>> On 04/29/2016 05:23 PM, Ramon Diaz-Uriarte wrote:
>>> Dear All,
>>>
>>> In case it matters, and since we are past the 22, I just noticed that a
>>> package I maintain (ADaCGH2) is giving warnings in Linux and Mac (e.g.,
>>> https://www.bioconductor.org/checkResults/devel/bioc-LATEST/ADaCGH2/zin2-checksrc.html)
>>> that, if I recall correctly, were not being given around the 22nd. I
>>> think
>>> these warnings have started appearing with the latest Rs in BioC
>>> (around
>>> r70549?). I haven't been able to understand the ultimate cause of the
>>> warnings (as they seem to refer to issues that are not in the code of
>>> my
>>> package), but they disappear when I move a package from Imports to
>>> Depends.
>>
>> They seem to come from GLAD's use of packageStartupMessage() in .onLoad
>> (e.g., when the package is imported) rather than the recommended
>> .onAttach (when the package is attached to the search() path, e.g., via
>> library() or Depends: in the DESCRIPTION file).
>>
>> I updated GLAD to use packageStartuupMessage() in .onAttach; I think the
>> warnings will go away.
>
> Martin, thanks for the reply and details. And sorry for my
> not-particularly-explicit message; yes, GLAD is the package that I moved
> to
> Depends. And I did not say (though I had intended too ---time to go to
> bed)
> that I had committed my changes to svn.
>
> Anyway, should I revert my changes to keep GLAD in Imports?
>
> Best,
>
> R.
>
>
>>
>> Martin
>>
>>>
>>>
>>> Best,
>>>
>>> R.
>>>
>>>
>>>
>>>
>>
>>
>> This email message may contain legally privileged and/or confidential
>> information.  If you are not the intended recipient(s), or the employee
>> or agent responsible for the delivery of this message to the intended
>> recipient(s), you are hereby notified that any disclosure, copying,
>> distribution, or use of this email message is prohibited.  If you have
>> received this message in error, please notify the sender immediately by
>> e-mail and delete this email message from your computer. Thank you.
>
>
> --
> Ramon Diaz-Uriarte
> Department of Biochemistry, Lab B-25
> Facultad de Medicina
> Universidad Autónoma de Madrid
> Arzobispo Morcillo, 4
> 28029 Madrid
> Spain
>
> Phone: +34-91-497-2412
>
> Email: rdia...@gmail.com
>ramon.d...@iib.uam.es
>
> http://ligarto.org/rdiaz
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel


-- 
Dipl.-Bioinf. Ludwig Geistlinger

Lehr- und Forschungseinheit für Bioinformatik
Institut für Informatik
Ludwig-Maximilians-Universität München
Amalienstrasse 17, 2. Stock, Büro A201
80333 München

Tel.: 089-2180-4067
eMail: ludwig.geistlin...@bio.ifi.lmu.de

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Re: [Bioc-devel] Update of data packages in RTCGA Family/Factory of R Packages

[Marcin Kosiński]

Thanks a lot! So I'll contact you after mid-May :)

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Re: [Bioc-devel] Making transcriptLength function a method in GenomicFeatures?

[Rainer Johannes]

Hi Herve,

passing down additional arguments to the internal exonsBy, cdsBy, 
fiveUTRsByTranscript and threeUTRsByTranscript would do it! That would be 
great, thanks.

cheers, jo

> On 02 May 2016, at 07:38, Hervé Pagès  wrote:
> 
> Hi Johannes,
> 
> We can make transcriptLengths() a generic but isn't the situation
> similar to the extractTranscriptSeqs() situation that you brought
> in January 
> (https://stat.ethz.ch/pipermail/bioc-devel/2016-January/008570.html) for 
> which adding the ellipsis to the argument list of the
> function and proper forwarding of the extra arguments did the trick?
> In the case of transcriptLengths() the extra arguments would be
> forwarded to the internal calls to transcripts(), exonsBy(), cdsBy(),
> fiveUTRsByTranscript(), and threeUTRsByTranscript(), and so
> transcriptLengths() would work out-of-the-box on EnsDb objects.
> Would that work?
> 
> H.
> 
> On 04/30/2016 04:05 AM, Rainer Johannes wrote:
>> Dear all,
>> 
>> I was wondering, you think it would be possible to make the transcriptLength 
>> function in GenomicFeatures a method and export that? Reason is that I have 
>> also implemented a transcriptLength function (actually presently a method in 
>> order to allow that to be used for EnsDb and TxDb objects), but this causes 
>> the warning
>> 
>> The following object is masked from 'package:GenomicFeatures':
>> 
>> transcriptLengths
>> 
>> on package loading.
>> 
>> Just in case, that’s the code from my package:
>> 
>> if(!isGeneric("transcriptLengths"))
>> setGeneric("transcriptLengths", function(x, with.cds_len=FALSE,
>>  with.utr5_len=FALSE,
>>  with.utr3_len=FALSE, ...)
>> standardGeneric("transcriptLengths”))
>> setMethod("transcriptLengths", "EnsDb", function(x, with.cds_len=FALSE, 
>> with.utr5_len=FALSE,
>> with.utr3_len=FALSE, 
>> filter=list()){
>> return(.transcriptLengths(x, with.cds_len=with.cds_len, 
>> with.utr5_len=with.utr3_len,
>>   with.utr3_len=with.utr3_len, filter=filter))
>> })
>> 
>> 
>> cheers, jo
>> 
>> 
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> 
> 
> -- 
> Hervé Pagès
> 
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
> 
> E-mail: hpa...@fredhutch.org
> Phone:  (206) 667-5791
> Fax:(206) 667-1319

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