Re: [Rd] R-devel internal errors during check produce?

[Jan Gorecki]

So the unique.default is from the R tools package during checks.
I don't see those issues on CRAN checks.
Exact environment where I am reproducing this issue is a fresh ubuntu,
no R packages pre-installed
docker pull registry.gitlab.com/jangorecki/dockerfiles/r-devel
https://gitlab.com/jangorecki/dockerfiles/-/raw/master/r-devel/Dockerfile

On Sat, Jun 27, 2020 at 12:37 AM Jan Gorecki  wrote:
>
> Hi R developers,
>
> On R-devel (2020-06-24 r78746) I am getting those two new exceptions
> during R check. I found a change which eventually may be related
> https://github.com/wch/r-source/commit/69de92b9fb1b7f2a7c8d1394b8d56050881a5465
> I think this may be a regression. I grep'ed package manuals and R code
> for unique.default but don't see any. Usage section of the unique
> method looks fine as well. Errors look a little bit like internal
> errors.
>
> * checking Rd \usage sections ... NOTE
>  Error in unique.default(env_list) :
>LENGTH or similar applied to environment object
>  Calls:  ... .get_S3_generics_as_seen_from_package ->
> unique -> unique.default
>  Execution halted
>  The \usage entries for S3 methods should use the \method markup and not
>  their full name.
>  * checking S3 generic/method consistency ... WARNING
>  Error in unique.default(env_list) :
>LENGTH or similar applied to environment object
>  Calls:  ... .get_S3_generics_as_seen_from_package ->
> unique -> unique.default
>
> I don't think if it is related but I build R-devel with extra args:
> --with-recommended-packages --enable-strict-barrier --disable-long-double
> I check with:
> --as-cran --no-manual
> To reproduce download current data.table from CRAN (1.12.8) and run R check
>
> Best regards,
> Jan Gorecki

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[Rd] R-devel internal errors during check produce?

[Jan Gorecki]

Hi R developers,

On R-devel (2020-06-24 r78746) I am getting those two new exceptions
during R check. I found a change which eventually may be related
https://github.com/wch/r-source/commit/69de92b9fb1b7f2a7c8d1394b8d56050881a5465
I think this may be a regression. I grep'ed package manuals and R code
for unique.default but don't see any. Usage section of the unique
method looks fine as well. Errors look a little bit like internal
errors.

* checking Rd \usage sections ... NOTE
 Error in unique.default(env_list) :
   LENGTH or similar applied to environment object
 Calls:  ... .get_S3_generics_as_seen_from_package ->
unique -> unique.default
 Execution halted
 The \usage entries for S3 methods should use the \method markup and not
 their full name.
 * checking S3 generic/method consistency ... WARNING
 Error in unique.default(env_list) :
   LENGTH or similar applied to environment object
 Calls:  ... .get_S3_generics_as_seen_from_package ->
unique -> unique.default

I don't think if it is related but I build R-devel with extra args:
--with-recommended-packages --enable-strict-barrier --disable-long-double
I check with:
--as-cran --no-manual
To reproduce download current data.table from CRAN (1.12.8) and run R check

Best regards,
Jan Gorecki

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[Rd] Error in substring: invalid multibyte string

[Toby Hocking]

Hi all,
I'm getting the following error from substring:

> substr("Jens Oehlschl\xe4gel-Akiyoshi", 1, 100)
Error in substr("Jens Oehlschl\xe4gel-Akiyoshi", 1, 100) :
  invalid multibyte string at 'gel-A<6b>iyoshi'

Is that normal / intended? I've tried setting the Encoding/locale to
Latin-1/UTF-8 but that does not help. nchar gives me something similar

> nchar("Jens Oehlschl\xe4gel-Akiyoshi")
Error in nchar("Jens Oehlschl\xe4gel-Akiyoshi") :
  invalid multibyte string, element 1

I find it strange that substr/nchar give an error but regexpr works for
telling me the length:

> regexpr(".*", "Jens Oehlschl\xe4gel-Akiyoshi")
[1] 1
attr(,"match.length")
[1] 29

Is that inconsistency normal/intended?

btw this example comes from our very own list:

> readLines("
https://stat.ethz.ch/pipermail/r-devel/1999-November/author.html;)[28]
[1] "Jens Oehlschl\xe4gel-Akiyoshi"

Best,
Toby

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[Rd] Change in lapply's missing argument passing

[William Dunlap via R-devel]

Consider the following expression, in which we pass 'i=', with no value
given for the 'i' argument, to lapply.
lapply("x", function(i, j) c(i=missing(i),j=missing(j), i=)
>From R-2.14.0 (2011-10-31) through R-3.4.4 (2018-03-15) this evaluated to
c(i=TRUE, j=FALSE).  From R-3.5.0 (2018-04-23) through R-4.0.0 (2020-04-24)
this evaluated to c(i=FALSE, j=TRUE).

Was this change intentional?

Bill Dunlap
TIBCO Software
wdunlap tibco.com

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Re: [R-pkg-devel] error when submit a package

[Guo, Wei (NIH/NIMH) [C] via R-package-devel]

Thank you all for the help. I do ask a question about a package _outside of 
CRAN yesterday. But I have new questions today about the global variable 
undefined, which was read from an Rdata object.

Thank you for your kind help again.
Best,
Wei

-Original Message-
From: Dirk Eddelbuettel  
Sent: Friday, June 26, 2020 5:23 PM
To: Zehao Xu 
Cc: Bert Gunter ; Guo, Wei (NIH/NIMH) [C] 
; r-package-devel@r-project.org
Subject: Re: [R-pkg-devel] error when submit a package


On 26 June 2020 at 19:16, Zehao Xu wrote:
| Package suggested but not available for checking: 'actigraphy'
| 
| ```
| 
| This stackoverflow 
| https://stackoverflow.com/questions/51453717/issue-with-r-package-chec
| k-on-windows-package-suggested-but-not-available-str can solve you 
| problem

No, wrong analysis. This SO answer is for _within CRAN_ depedency graphs.

Mr Guo has a problem with a package _outside of CRAN_ he chooses to depends 
upon. That will *never work*.

I answered on this list _just yesterday_ how I would address this, including a 
relevant peer-review reference. If Mr Gup chooses to ignore such advice and 
just spams us daily I suppose we may choose to ignore his emails. Oh well.

Dirk

--
http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

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Re: [R-pkg-devel] error when submit a package

[Dirk Eddelbuettel]

On 26 June 2020 at 19:16, Zehao Xu wrote:
| Package suggested but not available for checking: 'actigraphy'
| 
| ```
| 
| This stackoverflow 
https://stackoverflow.com/questions/51453717/issue-with-r-package-check-on-windows-package-suggested-but-not-available-str
 can solve you problem

No, wrong analysis. This SO answer is for _within CRAN_ depedency graphs.

Mr Guo has a problem with a package _outside of CRAN_ he chooses to depends
upon. That will *never work*.

I answered on this list _just yesterday_ how I would address this, including
a relevant peer-review reference. If Mr Gup chooses to ignore such advice and
just spams us daily I suppose we may choose to ignore his emails. Oh well.

Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

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Re: [R-pkg-devel] error when submit a package

[Paul Hibbing]

* The fourth can likely be addressed by if(getRversion() >= "2.15.1")
utils::globalVariables(c("IV", "M", "filename2id", "wear_flag"))

See https://github.com/tidyverse/magrittr/issues/29

* The fifth suggests you need to replace the default vignette title
with something specific to your package.

* The sixth (on Debian) could be fixed by adding
STUDYNAME_part0.maincall.R to .Rbuildignore. But the filename suggests
you need that file in your R directory, not ignored...

Hope that helps.
-Paul

On Fri, Jun 26, 2020 at 3:21 PM Zehao Xu  wrote:
>
> Well,
>
>
> The first note can be ignored (Note that you are the maintainer),
>
>
> the second one
>
> ```
>
> Maintainer: 'Wei Guoi '
>   Authors@R:  'Wei Guo '
>
> ```
>
> clearly, you miss spelled your name...
>
>
> the third one,
>
> ```
>
> checking package dependencies ... NOTE
> Package suggested but not available for checking: 'actigraphy'
>
> ```
>
> This stackoverflow 
> https://stackoverflow.com/questions/51453717/issue-with-r-package-check-on-windows-package-suggested-but-not-available-str
>  can solve you problem
>
>
>
> the fourth one
>
> ```
>
> IV_long2: no visible binding for global variable 'IV'
> Time_long2: no visible global function definition for 'wear_flag'
>
> ```
>
> It looks like you are using some variables not well defined in your 
> namespace, try to search "IV" and "wear_flag" in your package. Both of them 
> seem missing somehow.
>
>
> the fifth
>
> ```
>
> Package vignette with placeholder title 'Vignette Title':
>
> ```
>
> To be honest, I have no idea. What I suppose is that you use some illegal 
> chars in your vignette title.  It would be helpful if your share your 
> rmakrdown ymal.
>
>
> Best
>
> Zehao
>
> 
> From: R-package-devel  on behalf of 
> Bert Gunter 
> Sent: Friday, June 26, 2020 3:55:44 PM
> To: Guo, Wei (NIH/NIMH) [C]
> Cc: r-package-devel@r-project.org
> Subject: Re: [R-pkg-devel] error when submit a package
>
> Did you not post this before and receive answers? Please explain why the
> previous answers were insufficient. "Some notes are not fixable" is not a
> satisfactory response.
>
>
> Bert Gunter
>
> "The trouble with having an open mind is that people keep coming along and
> sticking things into it."
> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>
>
> On Fri, Jun 26, 2020 at 11:50 AM Guo, Wei (NIH/NIMH) [C] via
> R-package-devel  wrote:
>
> > Good afternoon,
> >
> > I am trying to submit my package to CRAN, and it failed to pass the checks
> > due to 5 notes. I am wondering how to fix it.
> >
> > Within the 5 notes, some are not fixable.
> > Thanks.
> > Best,
> > Wei
> >
> >
> >
> > Dear maintainer,
> >
> > package postGGIR_2.0.0.tar.gz does not pass the incoming checks
> > automatically, please see the following pre-tests:
> >
> > Windows: <
> > https://win-builder.r-project.org/incoming_pretest/postGGIR_2.0.0_20200626_200952/Windows/00check.log
> > >
> >
> > Status: 5 NOTEs
> >
> > Debian: <
> > https://win-builder.r-project.org/incoming_pretest/postGGIR_2.0.0_20200626_200952/Debian/00check.log
> > >
> >
> > Status: 6 NOTEs
> >
> >
> > ...
> > Wei Guo [C] | Biostatistician
> > National Institute of Mental Health (NIMH)
> > E-mail: wei.g...@nih.gov
> > Tel: 301-435-2206
> > 35 Convent Dr, Bethesda,MD,20892
> >
> >
> > [[alternative HTML version deleted]]
> >
> > __
> > R-package-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >
>
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>
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Re: [R-pkg-devel] error when submit a package

[Zehao Xu]

Well,


The first note can be ignored (Note that you are the maintainer),


the second one

```

Maintainer: 'Wei Guoi '
  Authors@R:  'Wei Guo '

```

clearly, you miss spelled your name...


the third one,

```

checking package dependencies ... NOTE
Package suggested but not available for checking: 'actigraphy'

```

This stackoverflow 
https://stackoverflow.com/questions/51453717/issue-with-r-package-check-on-windows-package-suggested-but-not-available-str
 can solve you problem



the fourth one

```

IV_long2: no visible binding for global variable 'IV'
Time_long2: no visible global function definition for 'wear_flag'

```

It looks like you are using some variables not well defined in your namespace, 
try to search "IV" and "wear_flag" in your package. Both of them seem missing 
somehow.


the fifth

```

Package vignette with placeholder title 'Vignette Title':

```

To be honest, I have no idea. What I suppose is that you use some illegal chars 
in your vignette title.  It would be helpful if your share your rmakrdown ymal.


Best

Zehao


From: R-package-devel  on behalf of Bert 
Gunter 
Sent: Friday, June 26, 2020 3:55:44 PM
To: Guo, Wei (NIH/NIMH) [C]
Cc: r-package-devel@r-project.org
Subject: Re: [R-pkg-devel] error when submit a package

Did you not post this before and receive answers? Please explain why the
previous answers were insufficient. "Some notes are not fixable" is not a
satisfactory response.


Bert Gunter

"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Fri, Jun 26, 2020 at 11:50 AM Guo, Wei (NIH/NIMH) [C] via
R-package-devel  wrote:

> Good afternoon,
>
> I am trying to submit my package to CRAN, and it failed to pass the checks
> due to 5 notes. I am wondering how to fix it.
>
> Within the 5 notes, some are not fixable.
> Thanks.
> Best,
> Wei
>
>
>
> Dear maintainer,
>
> package postGGIR_2.0.0.tar.gz does not pass the incoming checks
> automatically, please see the following pre-tests:
>
> Windows: <
> https://win-builder.r-project.org/incoming_pretest/postGGIR_2.0.0_20200626_200952/Windows/00check.log
> >
>
> Status: 5 NOTEs
>
> Debian: <
> https://win-builder.r-project.org/incoming_pretest/postGGIR_2.0.0_20200626_200952/Debian/00check.log
> >
>
> Status: 6 NOTEs
>
>
> ...
> Wei Guo [C] | Biostatistician
> National Institute of Mental Health (NIMH)
> E-mail: wei.g...@nih.gov
> Tel: 301-435-2206
> 35 Convent Dr, Bethesda,MD,20892
>
>
> [[alternative HTML version deleted]]
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>

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Re: [Bioc-devel] Unable to reproduce OS/X build error for "netDx" package

[Mike Smith]

Hi Shraddha,

I don't know what Java the build system uses, but I can reproduce the error
with Java 13.  It's fine with Java 8 as you say.

I wont copy the whole error message as it's the same as I see on the build
system, but I do notice that in the middle I see:

Java 8 detected

This seems wrong for my system:

> system2('java', '-version')
java version "13.0.2" 2020-01-14
Java(TM) SE Runtime Environment (build 13.0.2+8)
Java HotSpot(TM) 64-Bit Server VM (build 13.0.2+8, mixed mode, sharing)

Perhaps there's an issue with whatever part of the code is detecting the
version of java?

Mike


On Wed, 24 Jun 2020 at 18:10, Shraddha Pai 
wrote:

> Hi BioC community,
> My package relies on a Java jar and detects whether the OS has Java 8 or
> 11, to be accordingly compatible. I can't seem to resolve the build error
> on the BioC Mac system; the error message is a symptom of Java 8
> incompatibility.
>
> However, on my 2014 Mac Air which runs Java 8, the offending example
> ("Predict_CaseControl_from_CNV.Rmd") runs through to completion. What is
> the issue here? It would be great to have all operating systems building
> successfully.
>
> Details below. Thanks!
>
> Shraddha
> ---
> Error: This is the error: "WARNING: An illegal reflective access operation
> has occurred
>
> WARNING: Illegal reflective access by net.sf.cglib.core.ReflectUtils$2
>
> (file:/Users/biocbuild/Library/Caches/netDx/763502120e4_genemania-netdx.jar)
> to method
> java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
> WARNING: Please consider reporting this to the maintainers of
> net.sf.cglib.core.ReflectUtils$2"
>
> Mac specs: MacBook Air early 2014; High Sierra 10.13.6
>
> "java -version"  output:
> java version "1.8.0_31"
> Java(TM) SE Runtime Environment (build 1.8.0_31-b13)
> Java HotSpot(TM) 64-Bit Server VM (build 25.31-b07, mixed mode)
>
> R: 4.0.2 ; BioC 3.11
>
> sessionInfo output:
> > sessionInfo()
> R version 4.0.2 (2020-06-22)
> Platform: x86_64-apple-darwin17.0 (64-bit)
> Running under: macOS High Sierra 10.13.6
>
> Matrix products: default
> BLAS:
> /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
> LAPACK:
> /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
>
> locale:
> [1] C/C/C/C/C/en_CA.UTF-8
>
> attached base packages:
> [1] parallel  stats4stats graphics  grDevices utils datasets
> [8] methods   base
>
> other attached packages:
> [1] BiocFileCache_1.12.0 dbplyr_1.4.4 GenomicRanges_1.40.0
> [4] GenomeInfoDb_1.24.2  IRanges_2.22.2   S4Vectors_0.26.1
> [7] BiocGenerics_0.34.0  netDx_1.1.1  BiocStyle_2.16.0
>
> loaded via a namespace (and not attached):
>  [1] Biobase_2.48.0  httr_1.4.1
>  [3] splines_4.0.2   bit64_0.9-7
>  [5] foreach_1.5.0   R.utils_2.9.2
>  [7] assertthat_0.2.1BiocManager_1.30.10
>  [9] blob_1.2.1  GenomeInfoDbData_1.2.3
> [11] yaml_2.2.1  pillar_1.4.4
> [13] RSQLite_2.2.0   lattice_0.20-41
> [15] glue_1.4.1  digest_0.6.25
> [17] RColorBrewer_1.1-2  XVector_0.28.0
> [19] colorspace_1.4-1plyr_1.8.6
> [21] htmltools_0.5.0 Matrix_1.2-18
> [23] R.oo_1.23.0 XML_3.99-0.3
> [25] pkgconfig_2.0.3 bookdown_0.20
> [27] zlibbioc_1.34.0 purrr_0.3.4
> [29] scales_1.1.1MultiAssayExperiment_1.14.0
> [31] pracma_2.2.9combinat_0.0-8
> [33] tibble_3.0.1generics_0.0.2
> [35] ggplot2_3.3.2   ellipsis_0.3.1
> [37] SummarizedExperiment_1.18.1 ROCR_1.0-11
> [39] survival_3.1-12 RJSONIO_1.3-1.4
> [41] magrittr_1.5crayon_1.3.4
> [43] memoise_1.1.0   evaluate_0.14
> [45] R.methodsS3_1.8.0   doParallel_1.0.15
> [47] graph_1.66.0tools_4.0.2
> [49] lifecycle_0.2.0 matrixStats_0.56.0
> [51] stringr_1.4.0   glmnet_4.0-2
> [53] munsell_0.5.0   DelayedArray_0.14.0
> [55] compiler_4.0.2  rlang_0.4.6
> [57] grid_4.0.2  RCurl_1.98-1.2
> [59] iterators_1.0.12rappdirs_0.3.1
> [61] bigmemory.sri_0.1.3 igraph_1.2.5
> [63] bitops_1.0-6rmarkdown_2.3
> [65] gtable_0.3.0codetools_0.2-16
> [67] RCy3_2.8.0  DBI_1.1.0
> [69] curl_4.3reshape2_1.4.4
> [71] bigmemory_4.5.36R6_2.4.1
> [73] knitr_1.29  dplyr_1.0.0
> [75] bit_1.1-15.2shape_1.4.4
> [77] stringi_1.4.6   Rcpp_1.0.4.6
> [79] vctrs_0.3.1 tidyselect_1.1.0
> [81] xfun_0.15
>
>
> --
> Shraddha Pai, PhD
> http://shraddhapai.com ; @spaiglass on Twitter
> Post-doctoral Fellow, http://baderlab.org
> The Donnelly Centre for Cellular and Biomolecular Research
> University of Toronto
>
> [[alternative HTML version deleted]]
>
> 

Re: [R-pkg-devel] error when submit a package

[Bert Gunter]

Did you not post this before and receive answers? Please explain why the
previous answers were insufficient. "Some notes are not fixable" is not a
satisfactory response.


Bert Gunter

"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Fri, Jun 26, 2020 at 11:50 AM Guo, Wei (NIH/NIMH) [C] via
R-package-devel  wrote:

> Good afternoon,
>
> I am trying to submit my package to CRAN, and it failed to pass the checks
> due to 5 notes. I am wondering how to fix it.
>
> Within the 5 notes, some are not fixable.
> Thanks.
> Best,
> Wei
>
>
>
> Dear maintainer,
>
> package postGGIR_2.0.0.tar.gz does not pass the incoming checks
> automatically, please see the following pre-tests:
>
> Windows: <
> https://win-builder.r-project.org/incoming_pretest/postGGIR_2.0.0_20200626_200952/Windows/00check.log
> >
>
> Status: 5 NOTEs
>
> Debian: <
> https://win-builder.r-project.org/incoming_pretest/postGGIR_2.0.0_20200626_200952/Debian/00check.log
> >
>
> Status: 6 NOTEs
>
>
> ...
> Wei Guo [C] | Biostatistician
> National Institute of Mental Health (NIMH)
> E-mail: wei.g...@nih.gov
> Tel: 301-435-2206
> 35 Convent Dr, Bethesda,MD,20892
>
>
> [[alternative HTML version deleted]]
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>

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[R-pkg-devel] error when submit a package

[Guo, Wei (NIH/NIMH) [C] via R-package-devel]

Good afternoon,

I am trying to submit my package to CRAN, and it failed to pass the checks due 
to 5 notes. I am wondering how to fix it.

Within the 5 notes, some are not fixable.
Thanks.
Best,
Wei



Dear maintainer,

package postGGIR_2.0.0.tar.gz does not pass the incoming checks automatically, 
please see the following pre-tests:

Windows: 


Status: 5 NOTEs

Debian: 


Status: 6 NOTEs

...
Wei Guo [C] | Biostatistician
National Institute of Mental Health (NIMH)
E-mail: wei.g...@nih.gov
Tel: 301-435-2206
35 Convent Dr, Bethesda,MD,20892


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Re: [Bioc-devel] Deprecated a contained class

[Hervé Pagès]

Hi Martin,

Don't know how/where to implement a deprecation message that wouldn't be 
confusing for the end users.


FWIW if the replacement of class Original with class New is just a 
renaming (everything else remains the same), a situation I've dealt with 
a lot in the S4Vectors/IRanges/GenomicRanges infrastructure, I like to 
use the following pragmatic approach:


In package A:

  ## Replace Original with New in the Original class definition.
  setClass("New", ...)

  ## Define Original as an "alias" for New:
  setClass("Original", contains="New", representation("VIRTUAL"))

Then contact maintainers of packages that implement subclasses of 
Original that they should use New instead of Original. They can take 
their time because the cost of keeping the Original alias around is 
virtually zero.


H.

On 6/26/20 08:10, Martin Morgan wrote:

Pkg A provides a (virtual) class "Original".

Pkg B creates a derived class setClass("Derived", contains = "Original")

Pkg A would like to deprecate "Original" and replace with "New".

Any ideas on how to implement a deprecation message so that the Pkg B 
maintainer knows that their use of class Original is deprecated, but users 
aren't bothered by more-or-less incomprehensible messages on use? I guess using 
.Deprecated() somehow associated with setClass(); implementing something in 
initialize,Original-method would be too irritating to the user.

Thanks,

Martin

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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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Re: [Rd] R 4.0.1-4.0.2 built with Intel Composer 19.0-19.1.1, error in "make check" on CentOS 7.7

[Ryan Novosielski]

> On Jun 25, 2020, at 8:06 AM, Ivan Krylov  wrote:
> 
> On Wed, 24 Jun 2020 18:56:06 +
> Ryan Novosielski  wrote:
> 
> On my machine, getOption('expressions') is 5000 and the example from
> the test correctly stops with length(traceback()) == 2500. (And the
> simpler example of f <- function() f(); f() stops with
> length(traceback()) == 5000).
> 
>> Traceback:
> 
> <...>
> 
>> 2718: foo()
> 
> This (traceback() being more than 2500 entries long) seems to imply
> that the stack size check is somehow skipped. (Perhaps optimized away?)
> The evaluation depth limit is checked in src/main/eval.c, line 705 [*],
> followed by stack size check. Can you attach the debugger and take a
> look at the values of R_EvalDepth and R_Expressions while executing the
> text? What about R_CStackStart and R_CStackLimit? What is the stack
> size limit (ulimit -s?) on the machine running this test?

I can do that. I figure you may have more experience debugging R than I have, 
but I know the R command is a script, and that running the R binary directly 
doesn’t result in a working run. So what I’ve tried is to do “gdb /bin/bash” 
and then running R from that shell. Is that best/are there guidelines? I’m not 
much of an expert in this area. Is there also any special way I need to compile 
R to have the appropriate symbols?

The shell I’m running in had 8192 for stack size:

[novosirj@amarel-test1 R-4.0.2-intel-19.1-build]$ ulimit -s
8192

Thanks for your help!

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|| \\UTGERS, |---*O*---
||_// the State  | Ryan Novosielski - novos...@rutgers.edu
|| \\ University | Sr. Technologist - 973/972.0922 (2x0922) ~*~ RBHS Campus
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Re: [Rd] R 4.0.1-4.0.2 built with Intel Composer 19.0-19.1.1, error in "make check" on CentOS 7.7

[Ryan Novosielski]

> On Jun 25, 2020, at 10:31 AM, Bjørn-Helge Mevik  wrote:
> 
> Signed PGP part
> Ryan Novosielski  writes:
> 
>> Hi there,
>> 
>> I initially asked about this on r-help and was told this might be a better 
>> venue. I’m not really convinced from reading the posting guide, but I’ll 
>> give it a shot. It was also suggested that the R-Project doesn’t really care 
>> about building with “non-standard” compilers, but I can’t find any evidence 
>> of that on the website (indeed, there’s some mention of successful past 
>> builds, and the build itself is successful).
>> 
>> I built R 4.0.2 with the Intel Parallel Studio XE compiler suite, versions 
>> 19.0.x to 19.1.1. Build seems to go fine. I built it like this:
>> 
>> module purge
>> module load intel/19.1.1
>> module list
>> 
>> export CC=icc
>> export CXX=icpc
>> export F77=ifort
>> export FC=ifort
>> export AR=xiar
>> export LD=xild
>> 
>> export CFLAGS="-O3 -ipo -qopenmp -axAVX,CORE-AVX2,CORE-AVX512"
>> export F77FLAGS="-O3 -ipo -qopenmp -axAVX,CORE-AVX2,CORE-AVX512"
>> export FFLAGS="-O3 -ipo -qopenmp -axAVX,CORE-AVX2,CORE-AVX512"
>> export CXXFLAGS="-O3 -ipo -qopenmp -axAVX,CORE-AVX2,CORE-AVX512"
>> export MKL="-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread"
>> 
>> VERSION=4.0.1
>> 
>> /scratch/novosirj/install-files/R-${VERSION}/configure --with-blas="$MKL" 
>> --with-lapack --prefix=/opt/sw/packages/intel-19_1/R-Project/${VERSION} && \
>>   make -j32 && make check && make -j32 install
> 
> For what it is worth, we used to build R with the Intel compilers and
> MKL on our HPC cluster (on CentOS Linux), and we used the following
> setup.  Note the comments about -fp-model precise and -ipo.  It might no
> longer be a problem, but maybe worth checking.
> 
> fast="-ip -O3 -qopt-mem-layout-trans=3 -xHost -mavx"
> ## Notes:
> ## -static and -ipo break compilation
> ## -no-prec-div breaks make check
> ## -fp-model precise is needed for make check
> ## -wd188 removes a lot of warnings (see R Inst. & Adm. manual)
> export CC="icc"
> export CFLAGS="$fast -wd188 -fp-model precise"
> export F77="ifort"
> export FFLAGS="$fast -fp-model precise"
> export CXX="icpc"
> export CXXFLAGS="$fast -fp-model precise"
> export FC="ifort"
> export FCFLAGS="$fast -fp-model precise"
> 
> ## This works with intel 2011.10, at least:
> BLAS=--with-blas='-mkl=parallel'
> LAPACK=--with-lapack
> 
> ## To make the linker find libraries in modules:
> export LDFLAGS=$(echo $LD_LIBRARY_PATH | sed 's/^/-L/; s/:/ -L/g')
> 
> ./configure "$BLAS" "$LAPACK" --enable-BLAS-shlib --enable-R-shlib
> make -j 8
> make check
> make install

Thanks, Bjørn; -ipo no longer breaks compilation (I didn’t specify it, but I 
see that it was getting added automatically). I was really hoping that 
"-fp-model precise” (which also implies -prec-div which would seem to affect 
the other option mentioned) would have an impact on “make check” here, but 
apparently not. Also -wd188 is no longer required to hide warnings; this 
doesn’t seem to be happening anymore (but remember it myself from earlier on).

I guess it might make sense to check with Intel; we have support. I wish I 
could remember if this ever worked right, but I don’t think I thought/knew to 
run "make check" on our older builds.

--

|| \\UTGERS, |---*O*---
||_// the State  | Ryan Novosielski - novos...@rutgers.edu
|| \\ University | Sr. Technologist - 973/972.0922 (2x0922) ~*~ RBHS Campus
||  \\of NJ  | Office of Advanced Research Computing - MSB C630, Newark
 `'



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[Bioc-devel] Deprecated a contained class

[Martin Morgan]

Pkg A provides a (virtual) class "Original".

Pkg B creates a derived class setClass("Derived", contains = "Original")

Pkg A would like to deprecate "Original" and replace with "New".

Any ideas on how to implement a deprecation message so that the Pkg B 
maintainer knows that their use of class Original is deprecated, but users 
aren't bothered by more-or-less incomprehensible messages on use? I guess using 
.Deprecated() somehow associated with setClass(); implementing something in 
initialize,Original-method would be too irritating to the user.

Thanks,

Martin

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