Re: [Bioc-devel] Devel landing page version not updated after successful build

[Obenchain, Valerie]

Hi Raymond,

I think this is my fault. I accidentally turned off the cronjob that
refreshes/syncs the experiment data repos on the master builder. The job
has been reinstated and should run for today's builds. Thanks for
catching this and sorry for the inconvenience.

Valerie


On 04/11/2017 12:25 PM, Raymond Cavalcante wrote:
> Hello,
>
> As an additional wrinkle to this problem, I think that the builds for 
> chipenrich are still using chipenrich.data v1.11.6 instead of the successful 
> chipenrich.data v1.99.10. When I look at the R CMD check errors, I strongly 
> suspect it's because the wrong version of chipenrich.data is being used. 
> Orthogonally, the Travis builds that I have setup for these packages using 
> Rdevel appear to be fine.
>
> Thanks for any advice,
> Raymond Cavalcante
>
>> On Apr 11, 2017, at 10:32 AM, Raymond Cavalcante  wrote:
>>
>> Hello,
>>
>> I updated the devel version of chipenrich.data (an experiment package) and 
>> got a successful build for v1.99.10 
>> (http://bioconductor.org/checkResults/3.5/data-experiment-LATEST/chipenrich.data/
>>  
>> ),
>>  but the devel landing page doesn't reflect the change in version 
>> (http://bioconductor.org/packages/3.5/data/experiment/html/chipenrich.data.html
>>  
>> );
>>  instead, the given version is v1.11.6.
>>
>> I vaguely remember the landing page being quicker to update after a 
>> successful build, so I wanted to check in to see if I should be patient, if 
>> I've made a mistake, or there is something in the background that I need 
>> someone's help to fix.
>>
>> Thanks!
>> Raymond Cavalcante
>
>   [[alternative HTML version deleted]]
>
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Re: [Bioc-devel] Devel landing page version not updated after successful build

[Raymond Cavalcante]

Hello,

As an additional wrinkle to this problem, I think that the builds for 
chipenrich are still using chipenrich.data v1.11.6 instead of the successful 
chipenrich.data v1.99.10. When I look at the R CMD check errors, I strongly 
suspect it's because the wrong version of chipenrich.data is being used. 
Orthogonally, the Travis builds that I have setup for these packages using 
Rdevel appear to be fine.

Thanks for any advice,
Raymond Cavalcante

> On Apr 11, 2017, at 10:32 AM, Raymond Cavalcante  wrote:
> 
> Hello,
> 
> I updated the devel version of chipenrich.data (an experiment package) and 
> got a successful build for v1.99.10 
> (http://bioconductor.org/checkResults/3.5/data-experiment-LATEST/chipenrich.data/
>  
> ),
>  but the devel landing page doesn't reflect the change in version 
> (http://bioconductor.org/packages/3.5/data/experiment/html/chipenrich.data.html
>  
> );
>  instead, the given version is v1.11.6.
> 
> I vaguely remember the landing page being quicker to update after a 
> successful build, so I wanted to check in to see if I should be patient, if 
> I've made a mistake, or there is something in the background that I need 
> someone's help to fix.
> 
> Thanks!
> Raymond Cavalcante


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Re: [Rd] Poor documentation for "adj" and text()

[frederik]

Thanks Ulrich for sharing your experience.

I'm attaching a patch which tries to address the issues you raised.

I agree with you in principle, but I think it makes sense to leave
some details under "Details". However, the descriptions in "Arguments"
should give enough information that a user can get the function to do
something predictable in at least one situation, and I feel this is
not the case at present.

I tried to fix the wording so that 'adj' and 'offset' are no longer
confusing to new users (or to me, every time I forget what they mean).

I also fixed the paragraph on rotated text; it is more correct now, at
least for X11-cairo.

I hope that someone in the Core Team can look this over and apply it.

Thank you,

Frederick

On Tue, Apr 11, 2017 at 09:23:50AM +0200, Ulrich Windl wrote:
> Hi!
> 
> (I'd like to be able to access your bugzilla, BTW)
> The documentation for parameter "adj" of text() in R 3.3.3 is hard to 
> understand (unless you know what it does already):
> 
> "adj 
> one or two values in [0, 1] which specify the x (and optionally y) adjustment 
> of the labels. On most devices values outside that interval will also work."
> 
> What is the meaning of the values? I think the description ("adj allows 
> adjustment of the text with respect to (x, y). Values of 0, 0.5, and 1 
> specify left/bottom, middle and right/top alignment, respectively. The 
> default is for centered text, i.e., adj = c(0.5, NA). Accurate vertical 
> centering needs character metric information on individual characters which 
> is only available on some devices. Vertical alignment is done slightly 
> differently for character strings and for expressions: adj = c(0,0) means to 
> left-justify and to align on the baseline for strings but on the bottom of 
> the bounding box for expressions. This also affects vertical centering: for 
> strings the centering excludes any descenders whereas for expressions it 
> includes them. Using NA for strings centers them, including descenders.") 
> should be moved to the parameter.
> 
> In general I'd suggest to describe the range, meaning and default of every 
> parameter where the parameter is listed. "Details" should only give an 
> overview of the functions.
> 
> Likewise "offset": Will the direction be influenced by "pos"? The description 
> is quite silent on that.
> 
> Documentation should be structured to help the user to find the facts easily 
> without having to read the whole page.
> 
> Regards,
> Ulrich Windl
> 
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
> 
--- text.Rd	2016-11-27 18:33:26.541516325 -0800
+++ new-text.Rd	2017-04-11 11:48:32.668926075 -0700
@@ -26,16 +26,18 @@
 If \code{labels} is longer than \code{x} and
 \code{y}, the coordinates are recycled to the length of \code{labels}.}
   \item{adj}{one or two values in \eqn{[0, 1]} which specify the x
-(and optionally y) adjustment of the labels.  On most devices values
-outside that interval will also work.}
+(and optionally y) justification of the labels, with 0 for
+left/bottom, 1 for right/top, and 0.5 for centered.
+On most devices values
+outside \eqn{[0, 1]} will also work. See below.}
   \item{pos}{a position specifier for the text.  If specified this
 overrides any \code{adj} value given.  Values of \code{1},
 \code{2}, \code{3} and \code{4}, respectively indicate
 positions below, to the left of, above and to the right of
-the specified coordinates.}
-  \item{offset}{when \code{pos} is specified, this value gives the
-offset of the label from the specified coordinate in fractions
-of a character width.}
+\code{(x, y)}.}
+  \item{offset}{when \code{pos} is specified, this value controls the
+distance of the text label from \code{(x, y)}, in fractions of a
+character width.}
   \item{vfont}{\code{NULL} for the current font family, or a character
 vector of length 2 for Hershey vector fonts.  The first element of
 the vector selects a typeface and the second element selects a
@@ -62,10 +64,11 @@
   mathematical notation is available such as sub- and superscripts,
   greek letters, fractions, etc.
 
-  \code{adj} allows \emph{adj}ustment of the text with respect to
+  \code{adj} allows \emph{adj}ustment of the text position with respect to
   \code{(x, y)}.
-  Values of 0, 0.5, and 1 specify left/bottom, middle and
-  right/top alignment, respectively.  The default is for centered text, i.e.,
+  Values of 0, 0.5, and 1 specify that \code{(x, y)} should align with
+  the left/bottom, middle and
+  right/top of the text, respectively.  The default is for centered text, i.e.,
   \code{adj = c(0.5, NA)}.  Accurate vertical centering needs
   character metric information on individual characters which is
   only available on some devices.  Vertical alignment is done slightly
@@ -81,8 +84,17 @@
   labelled plot.
 
   Text can be rotated by using 

Re: [Bioc-devel] Fwd: Gostats and custom list

[amit kumar subudhi]

Sorry and thanks for the information.

On 11 Apr 2017 6:00 p.m., "James W. MacDonald"  wrote:

> This list is intended for discussions about package development, not
> general queries. Please post that sort of question on the support site,
> https://support.bioconductor.org
>
> On Tue, Apr 11, 2017 at 8:32 AM, amit kumar subudhi 
> wrote:
>
>> Hi,
>>
>> I am using Gostats to perform GO enrichment from custom list of genes and
>> custom annotations. My annotation file looks like this
>> head (geneGO)
>>   GOterm evi   GeneID
>> 1 GO:0016020  ND PCHAS_010020
>> 2 GO:0016021  ND PCHAS_010020
>> 3 GO:0016020  ND PCHAS_010030
>> 4 GO:0016021  ND PCHAS_010030
>> 5 GO:0016020  ND PCHAS_010040
>> 6 GO:0016021  ND PCHAS_010040
>>
>> My hyperGtest result looks like this
>> >Over.bp.Phase_0_2 <-hyperGTest(params.bp.Phase_0_2 )
>> >Over.bp.Phase_0_2
>> Gene to GO BP Conditional test for over-representation
>> 228 GO BP ids tested (45 have p < 0.05)
>> Selected gene set size: 37
>> Gene universe size: 1707
>> Annotation package: Based on a GeneSetCollection Object
>> and my summary result looks like this
>>
>> enrichgobp.Phase_9_12 <-summary(Over.bp.Phase_9_12 )
>>GOBPID   Pvalue OddsRatioExpCount Count
>> Size  Term V8
>> 1  GO:0019362 4.441045e-05 17.239583  0.43350908 5   20
>> pyridine nucleotide metabolic process Phase_0_2
>> 2  GO:0046031 1.163932e-04 22.370370  0.28178090 4
>> 13 ADP metabolic process Phase_0_2
>> 3  GO:0006096 1.163932e-04 22.370370  0.28178090 4
>> 13glycolytic process Phase_0_2
>> 4  GO:0016052 1.163932e-04 22.370370  0.28178090 4
>> 13carbohydrate catabolic process Phase_0_2
>> 5  GO:0009185 1.604285e-04 20.121212  0.30345636 4   14
>> ribonucleoside diphosphate metabolic process Phase_0_2
>> 6  GO:0009135 1.604285e-04 20.121212  0.30345636 4   14   purine
>> nucleoside diphosphate metabolic process Phase_0_2
>> 7  GO:0043436 2.085503e-04  5.450461  2.21089631 9
>> 102 oxoacid metabolic process Phase_0_2
>> 8  GO:0006165 2.153810e-04 18.280992  0.32513181 4   15
>> nucleoside diphosphate phosphorylation Phase_0_2
>> 9  GO:0051186 1.523968e-03  7.114211  0.88680352 5
>> 42cofactor metabolic process Phase_0_2
>>
>> what am I suppose to do, If I want to retrieve the geneIDs associated with
>> each GOterms. The other information about params is
>>
>> params.bp.Phase_0_2<-GSEAGOHyperGParams(name="P.chabaudi",
>> geneSetCollection=gsc,geneIds=Phase_0_2
>> ,universeGeneIds=universe,ontology="BP",pvalueCutoff=0.05,
>> conditional=TRUE,
>> testDirection="over")
>>
>> Looking forward to hear from you.
>>
>> With best regards, Amit
>>
>> --
>> Amit Kumar Subudhi, PhD
>> Post Doctoral Research Scientist,
>> Pathogen Genomics Group,
>> Division of Biological and Environmental Sciences and Engineering,
>> Level 4, 4326-WS10, Building 2,
>> King Abdullah University of Science and Technology (KAUST),
>>
>> Thuwal 23955-6900, Kingdom of Saudi Arabia,
>> Phone: (+966 12) 808 0614 <+966%2012%20808%200614>
>> <+966%2012%20808%200614>, Mobile: (+966) 5
>> 40375986,
>> Email Address: amit.subu...@kaust.edu.sa
>>
>>
>>
>> --
>> Amit Kumar Subudhi, PhD
>> Post Doctoral Research Scientist,
>> Pathogen Genomics Group,
>> Division of Biological and Environmental Sciences and Engineering,
>> Level 4, 4326-WS10, Building 2,
>> King Abdullah University of Science and Technology (KAUST),
>>
>> Thuwal 23955-6900, Kingdom of Saudi Arabia,
>> Phone: (+966 12) 808 0614, Mobile: (+966) 5 40375986,
>> Email Address: amit.subu...@kaust.edu.sa
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>

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Re: [Bioc-devel] Fwd: Gostats and custom list

[James W. MacDonald]

This list is intended for discussions about package development, not
general queries. Please post that sort of question on the support site,
https://support.bioconductor.org

On Tue, Apr 11, 2017 at 8:32 AM, amit kumar subudhi 
wrote:

> Hi,
>
> I am using Gostats to perform GO enrichment from custom list of genes and
> custom annotations. My annotation file looks like this
> head (geneGO)
>   GOterm evi   GeneID
> 1 GO:0016020  ND PCHAS_010020
> 2 GO:0016021  ND PCHAS_010020
> 3 GO:0016020  ND PCHAS_010030
> 4 GO:0016021  ND PCHAS_010030
> 5 GO:0016020  ND PCHAS_010040
> 6 GO:0016021  ND PCHAS_010040
>
> My hyperGtest result looks like this
> >Over.bp.Phase_0_2 <-hyperGTest(params.bp.Phase_0_2 )
> >Over.bp.Phase_0_2
> Gene to GO BP Conditional test for over-representation
> 228 GO BP ids tested (45 have p < 0.05)
> Selected gene set size: 37
> Gene universe size: 1707
> Annotation package: Based on a GeneSetCollection Object
> and my summary result looks like this
>
> enrichgobp.Phase_9_12 <-summary(Over.bp.Phase_9_12 )
>GOBPID   Pvalue OddsRatioExpCount Count
> Size  Term V8
> 1  GO:0019362 4.441045e-05 17.239583  0.43350908 5   20
> pyridine nucleotide metabolic process Phase_0_2
> 2  GO:0046031 1.163932e-04 22.370370  0.28178090 4
> 13 ADP metabolic process Phase_0_2
> 3  GO:0006096 1.163932e-04 22.370370  0.28178090 4
> 13glycolytic process Phase_0_2
> 4  GO:0016052 1.163932e-04 22.370370  0.28178090 4
> 13carbohydrate catabolic process Phase_0_2
> 5  GO:0009185 1.604285e-04 20.121212  0.30345636 4   14
> ribonucleoside diphosphate metabolic process Phase_0_2
> 6  GO:0009135 1.604285e-04 20.121212  0.30345636 4   14   purine
> nucleoside diphosphate metabolic process Phase_0_2
> 7  GO:0043436 2.085503e-04  5.450461  2.21089631 9
> 102 oxoacid metabolic process Phase_0_2
> 8  GO:0006165 2.153810e-04 18.280992  0.32513181 4   15
> nucleoside diphosphate phosphorylation Phase_0_2
> 9  GO:0051186 1.523968e-03  7.114211  0.88680352 5
> 42cofactor metabolic process Phase_0_2
>
> what am I suppose to do, If I want to retrieve the geneIDs associated with
> each GOterms. The other information about params is
>
> params.bp.Phase_0_2<-GSEAGOHyperGParams(name="P.
> chabaudi",geneSetCollection=gsc,geneIds=Phase_0_2
> ,universeGeneIds=universe,ontology="BP",pvalueCutoff=0.
> 05,conditional=TRUE,
> testDirection="over")
>
> Looking forward to hear from you.
>
> With best regards, Amit
>
> --
> Amit Kumar Subudhi, PhD
> Post Doctoral Research Scientist,
> Pathogen Genomics Group,
> Division of Biological and Environmental Sciences and Engineering,
> Level 4, 4326-WS10, Building 2,
> King Abdullah University of Science and Technology (KAUST),
>
> Thuwal 23955-6900, Kingdom of Saudi Arabia,
> Phone: (+966 12) 808 0614 <+966%2012%20808%200614>, Mobile: (+966) 5
> 40375986,
> Email Address: amit.subu...@kaust.edu.sa
>
>
>
> --
> Amit Kumar Subudhi, PhD
> Post Doctoral Research Scientist,
> Pathogen Genomics Group,
> Division of Biological and Environmental Sciences and Engineering,
> Level 4, 4326-WS10, Building 2,
> King Abdullah University of Science and Technology (KAUST),
>
> Thuwal 23955-6900, Kingdom of Saudi Arabia,
> Phone: (+966 12) 808 0614, Mobile: (+966) 5 40375986,
> Email Address: amit.subu...@kaust.edu.sa
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>



-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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[Bioc-devel] Devel landing page version not updated after successful build

[Raymond Cavalcante]

Hello,

I updated the devel version of chipenrich.data (an experiment package) and got 
a successful build for v1.99.10 
(http://bioconductor.org/checkResults/3.5/data-experiment-LATEST/chipenrich.data/
 
),
 but the devel landing page doesn't reflect the change in version 
(http://bioconductor.org/packages/3.5/data/experiment/html/chipenrich.data.html 
);
 instead, the given version is v1.11.6.

I vaguely remember the landing page being quicker to update after a successful 
build, so I wanted to check in to see if I should be patient, if I've made a 
mistake, or there is something in the background that I need someone's help to 
fix.

Thanks!
Raymond Cavalcante
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[Bioc-devel] Fwd: Gostats and custom list

[amit kumar subudhi]

Hi,

I am using Gostats to perform GO enrichment from custom list of genes and
custom annotations. My annotation file looks like this
head (geneGO)
  GOterm evi   GeneID
1 GO:0016020  ND PCHAS_010020
2 GO:0016021  ND PCHAS_010020
3 GO:0016020  ND PCHAS_010030
4 GO:0016021  ND PCHAS_010030
5 GO:0016020  ND PCHAS_010040
6 GO:0016021  ND PCHAS_010040

My hyperGtest result looks like this
>Over.bp.Phase_0_2 <-hyperGTest(params.bp.Phase_0_2 )
>Over.bp.Phase_0_2
Gene to GO BP Conditional test for over-representation
228 GO BP ids tested (45 have p < 0.05)
Selected gene set size: 37
Gene universe size: 1707
Annotation package: Based on a GeneSetCollection Object
and my summary result looks like this

enrichgobp.Phase_9_12 <-summary(Over.bp.Phase_9_12 )
   GOBPID   Pvalue OddsRatioExpCount Count
Size  Term V8
1  GO:0019362 4.441045e-05 17.239583  0.43350908 5   20
pyridine nucleotide metabolic process Phase_0_2
2  GO:0046031 1.163932e-04 22.370370  0.28178090 4
13 ADP metabolic process Phase_0_2
3  GO:0006096 1.163932e-04 22.370370  0.28178090 4
13glycolytic process Phase_0_2
4  GO:0016052 1.163932e-04 22.370370  0.28178090 4
13carbohydrate catabolic process Phase_0_2
5  GO:0009185 1.604285e-04 20.121212  0.30345636 4   14
ribonucleoside diphosphate metabolic process Phase_0_2
6  GO:0009135 1.604285e-04 20.121212  0.30345636 4   14   purine
nucleoside diphosphate metabolic process Phase_0_2
7  GO:0043436 2.085503e-04  5.450461  2.21089631 9
102 oxoacid metabolic process Phase_0_2
8  GO:0006165 2.153810e-04 18.280992  0.32513181 4   15
nucleoside diphosphate phosphorylation Phase_0_2
9  GO:0051186 1.523968e-03  7.114211  0.88680352 5
42cofactor metabolic process Phase_0_2

what am I suppose to do, If I want to retrieve the geneIDs associated with
each GOterms. The other information about params is

params.bp.Phase_0_2<-GSEAGOHyperGParams(name="P.chabaudi",geneSetCollection=gsc,geneIds=Phase_0_2
,universeGeneIds=universe,ontology="BP",pvalueCutoff=0.05,conditional=TRUE,
testDirection="over")

Looking forward to hear from you.

With best regards, Amit

-- 
Amit Kumar Subudhi, PhD
Post Doctoral Research Scientist,
Pathogen Genomics Group,
Division of Biological and Environmental Sciences and Engineering,
Level 4, 4326-WS10, Building 2,
King Abdullah University of Science and Technology (KAUST),

Thuwal 23955-6900, Kingdom of Saudi Arabia,
Phone: (+966 12) 808 0614 <+966%2012%20808%200614>, Mobile: (+966) 5
40375986,
Email Address: amit.subu...@kaust.edu.sa



-- 
Amit Kumar Subudhi, PhD
Post Doctoral Research Scientist,
Pathogen Genomics Group,
Division of Biological and Environmental Sciences and Engineering,
Level 4, 4326-WS10, Building 2,
King Abdullah University of Science and Technology (KAUST),

Thuwal 23955-6900, Kingdom of Saudi Arabia,
Phone: (+966 12) 808 0614, Mobile: (+966) 5 40375986,
Email Address: amit.subu...@kaust.edu.sa

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Re: [Bioc-devel] Installing EBImage with custom packages dir?

[Shepherd, Lori]

You can always use biocLite(pkg  , lib="path/to/library") .  The lib path in 
biocLite defaults to the .libPaths()[1].  When you do .libPaths() upon opening 
R does your path appear that you set with the environment variables?



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Guillaume MULLER 
Sent: Tuesday, April 11, 2017 8:28:34 AM
To: Shepherd, Lori; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Installing EBImage with custom packages dir?

Hi,

Thanks for your answer.

The R_LIBS and R_LIBS_USER environment variables are already set in my 
~/.Renviron . They point to the correct location. But this latter is not 
selected when installing packages with biocLite()...

Cheers

GM
--
Guillaume MULLER, PhD
PRESANS - Remix Coworking - L'Appart
57 rue de Turbigo
75003 Paris
France
http://www.presans.com
http://feeds.feedburner.com/OYI/fr


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.
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Re: [Bioc-devel] Installing EBImage with custom packages dir?

[Guillaume MULLER]

Hi,

Thanks for your answer.

The R_LIBS and R_LIBS_USER environment variables are already set in my 
~/.Renviron . They point to the correct location. But this latter is not 
selected when installing packages with biocLite()...

Cheers

GM
-- 
Guillaume MULLER, PhD
PRESANS - Remix Coworking - L'Appart
57 rue de Turbigo
75003 Paris
France
http://www.presans.com
http://feeds.feedburner.com/OYI/fr

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Re: [Bioc-devel] Installing EBImage with custom packages dir?

[Shepherd, Lori]

If you are able to set environment variables or have a .bash_aliases,  you 
could set the R_LIBS or R_LIBS_USER environment variables to your desired path 
"~/.R/x86_64-pc-linux-gnu-library/3.1.2".  When these are set it should become 
the default path in .libPaths() when you start R.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Guillaume 
MULLER 
Sent: Monday, April 3, 2017 5:45:22 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Installing EBImage with custom packages dir?

Hi,

I've been installing EBImage several time these past months on multiple 
machines, using instructions at: 
http://bioconductor.org/packages/release/bioc/html/EBImage.html.

I've noticed a few strange things with the installer:

- When the installer installs the dependencies and one of them fails (e.g. 
"tiff" or "png", because the headers are not installed on the system), and I 
run again biocLite("EBImage"), then even the dependencies that previously 
installed successfully (I saw the "DONE (xxx)" line in the logs) are 
re-downloaded and re-installed...

- The script asks if I want to upgrade my packages. If I says yes, then the 
system-wide installation fails because I'm not root, thus the biocLite() asks 
if I want to install the packages in my "personal library". If I answer "yes", 
it installs the packages in the default personal library location 
("~/R/x86_64-pc-linux-gnu-library/3.2"), whereas I've hardcoded my personal 
library location by using (.libPaths("~/.R/x86_64-pc-linux-gnu-library/3.1.2" 
in my .Rprofile)... Also, I'm not sure the script does not takes into account 
the packages already installed installed in my personal library, thus 
redundantly (re)-installs some packages in the default location.

Is there any work-around so that I don't have to move all the (redundantly) 
installed packages into my actual personal library?

Cheers


GM
--
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PRESANS - Remix Coworking - L'Appart
57 rue de Turbigo
75003 Paris
France
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Re: [Rd] Downloader that Resolves library dependencies

[Dirk Eddelbuettel]

On 11 April 2017 at 13:01, Ulrich Windl wrote:
| If you want to install an extra library like "car", there is a long list of 
dependencies. If you just download "car", you cannot use it.
| Unfortunately the download links offer no solution to select all dependent 
libraries for download also. It would be nice, however.
| (This is interesting for people that want to use R in an Intranet that does 
not have Internet access)

The package system mechanism is really good, and has its kinked worked
out. He describe an additional constraint from your side ("no internet")
which makes downloading challenging in the first place.

But that question has been answered too, and many times over by now. Eg
http://stackoverflow.com/a/6281417/143305

Dirk

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Re: [Rd] Downloader that Resolves library dependencies

[Rui Barradas]

Hello,

Try ?install.packages from within R.

install.packages("car", dependencies = TRUE)

Hope this helps,

Rui Barradas

Em 11-04-2017 12:01, Ulrich Windl escreveu:

Hi!

If you want to install an extra library like "car", there is a long list of dependencies. 
If you just download "car", you cannot use it.
Unfortunately the download links offer no solution to select all dependent 
libraries for download also. It would be nice, however.
(This is interesting for people that want to use R in an Intranet that does not 
have Internet access)

Regards,
Ulrich

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[Rd] Downloader that Resolves library dependencies

[Ulrich Windl]

Hi!

If you want to install an extra library like "car", there is a long list of 
dependencies. If you just download "car", you cannot use it.
Unfortunately the download links offer no solution to select all dependent 
libraries for download also. It would be nice, however.
(This is interesting for people that want to use R in an Intranet that does not 
have Internet access)

Regards,
Ulrich

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[Rd] Poor documentation for "adj" and text()

[Ulrich Windl]

Hi!

(I'd like to be able to access your bugzilla, BTW)
The documentation for parameter "adj" of text() in R 3.3.3 is hard to 
understand (unless you know what it does already):

"adj 
one or two values in [0, 1] which specify the x (and optionally y) adjustment 
of the labels. On most devices values outside that interval will also work."

What is the meaning of the values? I think the description ("adj allows 
adjustment of the text with respect to (x, y). Values of 0, 0.5, and 1 specify 
left/bottom, middle and right/top alignment, respectively. The default is for 
centered text, i.e., adj = c(0.5, NA). Accurate vertical centering needs 
character metric information on individual characters which is only available 
on some devices. Vertical alignment is done slightly differently for character 
strings and for expressions: adj = c(0,0) means to left-justify and to align on 
the baseline for strings but on the bottom of the bounding box for expressions. 
This also affects vertical centering: for strings the centering excludes any 
descenders whereas for expressions it includes them. Using NA for strings 
centers them, including descenders.") should be moved to the parameter.

In general I'd suggest to describe the range, meaning and default of every 
parameter where the parameter is listed. "Details" should only give an overview 
of the functions.

Likewise "offset": Will the direction be influenced by "pos"? The description 
is quite silent on that.

Documentation should be structured to help the user to find the facts easily 
without having to read the whole page.

Regards,
Ulrich Windl

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Re: [Bioc-devel] Using BiocInstaller with R 3.4.0 beta

[Martin Morgan]

On 04/11/2017 05:01 AM, Gordon K Smyth wrote:

The problem appears to be with installed.packages(). If I start a fresh R 
3.4.0beta session, then I can run installed.packages() once with correct 
results, but running it a second time gives the error message:


installed.packages()

Error in if (file.exists(dest) && file.mtime(dest) > file.mtime(lib) &&  :
  missing value where TRUE/FALSE needed


The test is in this code chunk, from utils/R/packages.R

for(lib in lib.loc) {
if(noCache) {
ret0 <- .readPkgDesc(lib, fields)
if(length(ret0)) retval <- rbind(retval, ret0)
} else {
## Previously used URLencode for e.g. Windows paths with drives
## This version works for very long file names.
base <- paste(c(lib, fields), collapse = ",")
## add length and 64-bit CRC in hex (in theory, seems
## it is actually 32-bit on some systems)
enc <- sprintf("%d_%s", nchar(base), .Call(C_crc64, base))
dest <- file.path(tempdir(), paste0("libloc_", enc, ".rds"))
if(file.exists(dest) &&
   file.mtime(dest) > file.mtime(lib) &&
   (val <- readRDS(dest))$base == base)
## use the cache file
retval <- rbind(retval, val$value)
else {
ret0 <- .readPkgDesc(lib, fields)
if(length(ret0)) {
retval <- rbind(retval, ret0)
## save the cache file
saveRDS(list(base = base, value = ret0), dest)
}
}
}


where 'lib' is one of .libPaths(), 'dest' is one of

  dir(tempdir(), pattern="libloc_", full=TRUE)

and 'base' should be a character(1)

I think the code chunk has tried to cache the packages installed in each 
directory of .libPaths() (the saveRDS() line), and these are somehow 
corrupted on the second time through (I guess evaluating the readRDS()??).


For instance I have two paths in .libPaths() and after the first 
install.packages() I have


> str(readRDS(dir(tempdir(), full=TRUE)[1]))
List of 2
 $ base : chr 
"/home/mtmorgan/bin/R-3-4-branch/library,Version,Priority,Depends,Imports,LinkingTo,Suggests,Enhances,License,Li"| 
__truncated__

 $ value: chr [1:29, 1:17] "base" "boot" "class" "cluster" ...
> str(readRDS(dir(tempdir(), full=TRUE)[2]))
List of 2
 $ base : chr 
"/home/mtmorgan/R/x86_64-pc-linux-gnu-library/3.4-Bioc-3.5,Version,Priority,Depends,Imports,LinkingTo,Suggests,E"| 
__truncated__

 $ value: chr [1:513, 1:17] "abind" "acepack" "aCGH" "ADaCGH2" ...

I'm guessing that one of these files is corrupted somehow, but it's not 
obvious how. Can you use options(error=recover) and find the values that 
cause the conditional to fail?


Martin





-Original Message-
From: Gordon K Smyth
Sent: Tuesday, 11 April 2017 6:26 PM
To: bioc-devel@r-project.org
Subject: Using BiocInstaller with R 3.4.0 beta

I thought I would test out R 3.4.0 beta (for Windows) but now I can't use the
BiocInstaller package. Attempts to use biocLite() or biocValid() lead to an 
error
message as shown below.

What have I overlooked?

Thanks
Gordon


sessionInfo()

R version 3.4.0 beta (2017-04-08 r72499)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252
LC_MONETARY=English_Australia.1252
[4] LC_NUMERIC=C   LC_TIME=English_Australia.1252

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

loaded via a namespace (and not attached):
[1] compiler_3.4.0

remove.packages("BiocInstaller")

Removing package from 'C:/lib/R/R-3.4.0beta/library'
(as 'lib' is unspecified)
Error in find.package(pkgs, lib) :
  there is no package called 'BiocInstaller'

source("https://bioconductor.org/biocLite.R;)

trying URL
'https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.4/BiocInst
aller_1.25.3.zip'
Content type 'application/zip' length 127489 bytes (124 KB)
downloaded 124 KB

package 'BiocInstaller' successfully unpacked and MD5 sums checked

The downloaded binary packages are in

C:\Users\smyth\AppData\Local\Temp\RtmpOUhCbB\downloaded_packages
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help

BiocInstaller::biocValid()

Error in if (file.exists(dest) && file.mtime(dest) > file.mtime(lib) &&  :
  missing value where TRUE/FALSE needed


-
Professor Gordon K Smyth,
Head, Bioinformatics Division,
Walter and Eliza Hall Institute of Medical Research,
http://www.statsci.org/smyth


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Re: [Bioc-devel] Using BiocInstaller with R 3.4.0 beta

[Gordon K Smyth]

The problem appears to be with installed.packages(). If I start a fresh R 
3.4.0beta session, then I can run installed.packages() once with correct 
results, but running it a second time gives the error message:

> installed.packages()
Error in if (file.exists(dest) && file.mtime(dest) > file.mtime(lib) &&  : 
  missing value where TRUE/FALSE needed


> -Original Message-
> From: Gordon K Smyth
> Sent: Tuesday, 11 April 2017 6:26 PM
> To: bioc-devel@r-project.org
> Subject: Using BiocInstaller with R 3.4.0 beta
> 
> I thought I would test out R 3.4.0 beta (for Windows) but now I can't use the
> BiocInstaller package. Attempts to use biocLite() or biocValid() lead to an 
> error
> message as shown below.
> 
> What have I overlooked?
> 
> Thanks
> Gordon
> 
> > sessionInfo()
> R version 3.4.0 beta (2017-04-08 r72499)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> Running under: Windows 7 x64 (build 7601) Service Pack 1
> 
> Matrix products: default
> 
> locale:
> [1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252
> LC_MONETARY=English_Australia.1252
> [4] LC_NUMERIC=C   LC_TIME=English_Australia.1252
> 
> attached base packages:
> [1] stats graphics  grDevices utils datasets  methods   base
> 
> loaded via a namespace (and not attached):
> [1] compiler_3.4.0
> > remove.packages("BiocInstaller")
> Removing package from 'C:/lib/R/R-3.4.0beta/library'
> (as 'lib' is unspecified)
> Error in find.package(pkgs, lib) :
>   there is no package called 'BiocInstaller'
> > source("https://bioconductor.org/biocLite.R;)
> trying URL
> 'https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.4/BiocInst
> aller_1.25.3.zip'
> Content type 'application/zip' length 127489 bytes (124 KB)
> downloaded 124 KB
> 
> package 'BiocInstaller' successfully unpacked and MD5 sums checked
> 
> The downloaded binary packages are in
> 
> C:\Users\smyth\AppData\Local\Temp\RtmpOUhCbB\downloaded_packages
> Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
> > BiocInstaller::biocValid()
> Error in if (file.exists(dest) && file.mtime(dest) > file.mtime(lib) &&  :
>   missing value where TRUE/FALSE needed
> 
> 
> -
> Professor Gordon K Smyth,
> Head, Bioinformatics Division,
> Walter and Eliza Hall Institute of Medical Research,
> http://www.statsci.org/smyth

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[Bioc-devel] Using BiocInstaller with R 3.4.0 beta

[Gordon K Smyth]

I thought I would test out R 3.4.0 beta (for Windows) but now I can't use the 
BiocInstaller package. Attempts to use biocLite() or biocValid() lead to an 
error message as shown below.

What have I overlooked?

Thanks
Gordon

> sessionInfo()
R version 3.4.0 beta (2017-04-08 r72499)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252
LC_MONETARY=English_Australia.1252
[4] LC_NUMERIC=C   LC_TIME=English_Australia.1252

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base 

loaded via a namespace (and not attached):
[1] compiler_3.4.0
> remove.packages("BiocInstaller")
Removing package from 'C:/lib/R/R-3.4.0beta/library'
(as 'lib' is unspecified)
Error in find.package(pkgs, lib) : 
  there is no package called 'BiocInstaller'
> source("https://bioconductor.org/biocLite.R;)
trying URL 
'https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.4/BiocInstaller_1.25.3.zip'
Content type 'application/zip' length 127489 bytes (124 KB)
downloaded 124 KB

package 'BiocInstaller' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
C:\Users\smyth\AppData\Local\Temp\RtmpOUhCbB\downloaded_packages
Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
> BiocInstaller::biocValid()
Error in if (file.exists(dest) && file.mtime(dest) > file.mtime(lib) &&  : 
  missing value where TRUE/FALSE needed


-
Professor Gordon K Smyth,
Head, Bioinformatics Division,
Walter and Eliza Hall Institute of Medical Research,
http://www.statsci.org/smyth

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[Bioc-devel] test coverage of a shiny app

[Samuel Wieczorek]

Hi

I am the developer of the packages Prostar ad DAPAR and I would like to 
write some unit test for Prostar which contains a Shiny application. I 
wrote a test script in the 'test' directory where I am using functions 
from the shiytest package but I don't know how to really test my app 
(Prostar()). And then, the result of packages_coverage is still equal to 0%.

Is there anyone who has already developed a Shiny app with unit tests ? 
I would appreciate some examples.


Thanks in advance


Sam


-- 
*Samuel Wieczorek

Etude de la Dynamique des Protéomes (EDyP)*
*Laboratoire Biologie à Grande Echelle (BGE)*
*U1038 INSERM / CEA / UGA*
*Biosciences and Biotechnology Institute of Grenoble (BIG)*
*CEA / Grenoble*
*17 avenue des Martyrs*
*F-38054 Grenoble Cedex 9*
*/Tél. : 04.38.78.44.14/*
*/Fax : 04.38.78.50.51/*

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Re: [Rd] Bug report: POSIX regular expression doesn't match for somewhat higher values of upper bound

[dietmar.schindler]

> Von: Martin Maechler [mailto:maech...@stat.math.ethz.ch]
> Gesendet: Mittwoch, 5. April 2017 11:15
>
> >   
> > on Tue, 4 Apr 2017 08:45:30 + writes:
>
> > Dear Sirs,
> > while
>
> >> regexpr('(.{1,2})\\1', 'foo')
> > [1] 2
> > attr(,"match.length")
> > [1] 2
> > attr(,"useBytes")
> > [1] TRUE
>
> > yields the correct match, an incremented upper bound in
>
> >> regexpr('(.{1,3})\\1', 'foo')
> > [1] -1
> > attr(,"match.length")
> > [1] -1
> > attr(,"useBytes")
> > [1] TRUE
>
> > incorrectly yields no match.
>
> Hmm, yes, I would also say that this is incorrect
> (though I'm always cautious: The  ?regex  help page explicitly
>  mentions greedy repetitions, and these can "bite you" ..)
>
> The behavior is also different from the  perl=TRUE one which is
> correct (according to the above understanding).
>
> ...

Shouldn't this be submitted on R's Bugzilla then (which I as a non-member 
can't)?
--
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Dietmar Schindler

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