Re: [Bioc-devel] error while trying to run BiocCheck

2018-03-03 Thread Martin Morgan 



On 03/03/2018 06:45 AM, Claris Baby via Bioc-devel wrote:

Dear all,I am trying to build a package for RNA-seq analysis combining 
different existing packages in bioconductor and am facing problem while trying 
to run

BiocCheck("/home/package_name", `no-check-vignettes`=TRUE)
The error generated is as follows:
This is BiocCheck version 1.14.0. BiocCheck is a work in progress. Output and 
severity of issues may
change. Installing package...
* Checking for version number mismatch...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
 * NOTE: Consider clarifying how 2 object(s) are initialized. Maybe they 
are part of a data set
   loaded with data(), or perhaps part of an object referenced in with() or 
within().
 object (function)
   DataFrame (gene_exp)
   count (gene_exp)
Error in dots[["no-check-vignettes"]] : subscript out of bounds


This seems like a bug in BiocCheck; to invoke interactively, use

  BiocCheck("/home/package_name", list(`no-check-vignettes`=TRUE))

or from the command line

  R CMD BiocCheck --no-check-vignettes /home/package_name

We'll try to address the problem shortly...

Martin


I have already added VignetteBuilder: knitr and Suggests: knitrIt would be very 
helpful if you could help solve this error and also the note mentioned above

Session infoR version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale:
  [1] LC_CTYPE=en_IN.UTF-8   LC_NUMERIC=C   LC_TIME=en_IN.UTF-8 
   LC_COLLATE=en_IN.UTF-8
  [5] LC_MONETARY=en_IN.UTF-8LC_MESSAGES=en_IN.UTF-8
LC_PAPER=en_IN.UTF-8   LC_NAME=C
  [9] LC_ADDRESS=C   LC_TELEPHONE=C 
LC_MEASUREMENT=en_IN.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats4parallel  stats graphics  grDevices utils datasets  
methods   base

other attached packages:
  [1] newtest_0.1.0  BiocCheck_1.14.0   biocViews_1.46.0
   biomaRt_2.32.1
  [5] knitr_1.19 Rqc_1.10.2 ggplot2_2.2.1   
   GenomicFeatures_1.28.5
  [9] AnnotationDbi_1.38.2   systemPipeR_1.10.2 ShortRead_1.34.1
   GenomicAlignments_1.12.2
[13] SummarizedExperiment_1.6.5 DelayedArray_0.2.7 matrixStats_0.53.1   
  Biobase_2.36.2
[17] BiocParallel_1.10.1Rsamtools_1.28.0   Biostrings_2.44.2
  XVector_0.16.0
[21] GenomicRanges_1.28.6   GenomeInfoDb_1.12.2IRanges_2.10.4   
  S4Vectors_0.14.6
[25] BiocGenerics_0.22.0

loaded via a namespace (and not attached):
   [1] backports_1.1.2   GOstats_2.42.0Hmisc_4.1-1
   [4] AnnotationHub_2.8.2   LSD_4.0-0 plyr_1.8.4
   [7] lazyeval_0.2.1GSEABase_1.38.2   splines_3.4.0
  [10] BatchJobs_1.7 easyRNASeq_2.12.1 digest_0.6.15
  [13] BiocInstaller_1.28.0  ensembldb_2.0.4   
htmltools_0.3.6
  [16] GO.db_3.4.1   gdata_2.18.0  magrittr_1.5
  [19] checkmate_1.8.5   memoise_1.1.0 BBmisc_1.11
  [22] BSgenome_1.44.2   cluster_2.0.6 DEXSeq_1.22.0
  [25] limma_3.32.7  annotate_1.54.0   
colorspace_1.3-2
  [28] blob_1.1.0RCurl_1.95-4.10   graph_1.54.0
  [31] genefilter_1.58.1 brew_1.0-6
survival_2.41-3
  [34] sendmailR_1.2-1   VariantAnnotation_1.22.3  ape_5.0
  [37] gtable_0.2.0  zlibbioc_1.22.0   scales_0.5.0
  [40] DESeq_1.28.0  pheatmap_1.0.8vsn_3.44.0
  [43] DBI_0.7   edgeR_3.18.1  Rcpp_0.12.15
  [46] xtable_1.8-2  htmlTable_1.11.2  
foreign_0.8-69
  [49] bit_1.1-12preprocessCore_1.38.1 Formula_1.2-2
  [52] intervals_0.15.1  AnnotationForge_1.18.2getopt_1.20.1
  [55] htmlwidgets_0.9   httr_1.3.1gplots_3.0.1
  [58] RColorBrewer_1.1-2acepack_1.4.1 
pkgconfig_2.0.1
  [61] reshape_0.8.7 XML_3.98-1.9  Gviz_1.20.0
  [64] nnet_7.3-12   locfit_1.5-9.1rlang_0.1.6
  [67] reshape2_1.4.3munsell_0.4.3 tools_3.4.0
  [70] qrqc_1.30.0   RSQLite_2.0   
evaluate_0.10.1
  [73] stringr_1.2.0 yaml_2.1.16   bit64_0.9-7
  [76] caTools_1.17.1AnnotationFilter_1.0.0ASpli_1.2.3
  [79] RBGL_1.52.0   nlme_3.1-131  mime_0.5
  [82] genomeIntervals_1.32.0BiocStyle_2.4.1

Re: [Bioc-devel] Updated Deprecated Package List for Bioc 3.7

2018-03-03 Thread Ludwig Geistlinger 
Hi Lori,


Yes I would take over maintenance.

Anything particular that I need to take care of?


Otherwise I would just follow:


https://bioconductor.org/developers/how-to/git/maintain-github-bioc/


to accordingly set this up.


Thanks,

Ludwig


--
Dr. Ludwig Geistlinger
CUNY School of Public Health

From: Shepherd, Lori 
Sent: Saturday, March 3, 2018 5:14 PM
To: Ludwig Geistlinger; Martin Morgan
Subject: Re: [Bioc-devel] Updated Deprecated Package List for Bioc 3.7


Hi Ludwig,


Were you still interested in taking over maintainership of ToPaSeq?  We have 
switched permission and you should have access now.  If you are no longer 
interested please let us know.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Ludwig Geistlinger 
Sent: Friday, December 15, 2017 1:05:16 PM
To: Shepherd, Lori; Martin Morgan
Subject: Re: [Bioc-devel] Updated Deprecated Package List for Bioc 3.7

Hi Lori,

I would be willing to take over maintenance of

ToPASeq

in case maintainers remain unresponsive.

Best,
Ludwig

--
Dr. Ludwig Geistlinger
CUNY School of Public Health


From: Bioc-devel  on behalf of Shepherd, Lori 

Sent: Friday, December 15, 2017 9:29 AM
To: Martin Morgan
Subject: [Bioc-devel] Updated Deprecated Package List for Bioc 3.7

The Bioconductor Team is continuing to identify packages that will be 
deprecated in the next release to allow for the Bioconductor community to 
respond accordingly. The list will be updated monthly.

The current list of deprecated packages is as follows:

Maintainer requested deprecation:

Software Package:
ontoCAT

Experiment Data Package:
RnaSeqTutorial
cheung2010



Unresponsive/not-maintained packages:

Software:
GMRP
MBttest
OperaMate
ToPASeq


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


This email message may contain legally privileged and/or confidential 
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recipient(s), you are hereby notified that any disclosure, copying, 
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this message in error, please notify the sender immediately by e-mail and 
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Re: [Bioc-devel] Updated Deprecated Package List for Bioc 3.7

2018-03-03 Thread Shepherd, Lori 
Hi Ludwig,


Were you still interested in taking over maintainership of ToPaSeq?  We have 
switched permission and you should have access now.  If you are no longer 
interested please let us know.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Ludwig Geistlinger 
Sent: Friday, December 15, 2017 1:05:16 PM
To: Shepherd, Lori; Martin Morgan
Subject: Re: [Bioc-devel] Updated Deprecated Package List for Bioc 3.7

Hi Lori,

I would be willing to take over maintenance of

ToPASeq

in case maintainers remain unresponsive.

Best,
Ludwig

--
Dr. Ludwig Geistlinger
CUNY School of Public Health


From: Bioc-devel  on behalf of Shepherd, Lori 

Sent: Friday, December 15, 2017 9:29 AM
To: Martin Morgan
Subject: [Bioc-devel] Updated Deprecated Package List for Bioc 3.7

The Bioconductor Team is continuing to identify packages that will be 
deprecated in the next release to allow for the Bioconductor community to 
respond accordingly. The list will be updated monthly.

The current list of deprecated packages is as follows:

Maintainer requested deprecation:

Software Package:
ontoCAT

Experiment Data Package:
RnaSeqTutorial
cheung2010



Unresponsive/not-maintained packages:

Software:
GMRP
MBttest
OperaMate
ToPASeq


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


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.
[[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 
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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[Bioc-devel] Single Package Builder temporarily down

2018-03-03 Thread Shepherd, Lori 
There have been some updates to the builders and will require some additional 
updates to the single package builder.  While this is occurring the single 
package builder for new package submissions will temporarily be down.  We will 
notify when the updates are complete and the single package builder back online.


Thank you for your patience


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


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.
[[alternative HTML version deleted]]

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[Bioc-devel] error while trying to run BiocCheck

2018-03-03 Thread Claris Baby via Bioc-devel 
Dear all,I am trying to build a package for RNA-seq analysis combining 
different existing packages in bioconductor and am facing problem while trying 
to run 

BiocCheck("/home/package_name", `no-check-vignettes`=TRUE)
The error generated is as follows:
This is BiocCheck version 1.14.0. BiocCheck is a work in progress. Output and 
severity of issues may
change. Installing package...
* Checking for version number mismatch...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* NOTE: Consider clarifying how 2 object(s) are initialized. Maybe they are 
part of a data set
  loaded with data(), or perhaps part of an object referenced in with() or 
within().
object (function)
  DataFrame (gene_exp)
  count (gene_exp)
Error in dots[["no-check-vignettes"]] : subscript out of bounds
I have already added VignetteBuilder: knitr and Suggests: knitrIt would be very 
helpful if you could help solve this error and also the note mentioned 
above 

Session infoR version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale:
 [1] LC_CTYPE=en_IN.UTF-8   LC_NUMERIC=C   LC_TIME=en_IN.UTF-8  
  LC_COLLATE=en_IN.UTF-8
 [5] LC_MONETARY=en_IN.UTF-8LC_MESSAGES=en_IN.UTF-8LC_PAPER=en_IN.UTF-8 
  LC_NAME=C 
 [9] LC_ADDRESS=C   LC_TELEPHONE=C 
LC_MEASUREMENT=en_IN.UTF-8 LC_IDENTIFICATION=C   

attached base packages:
[1] stats4parallel  stats graphics  grDevices utils datasets  
methods   base 

other attached packages:
 [1] newtest_0.1.0  BiocCheck_1.14.0   biocViews_1.46.0 
  biomaRt_2.32.1
 [5] knitr_1.19 Rqc_1.10.2 ggplot2_2.2.1
  GenomicFeatures_1.28.5
 [9] AnnotationDbi_1.38.2   systemPipeR_1.10.2 ShortRead_1.34.1 
  GenomicAlignments_1.12.2  
[13] SummarizedExperiment_1.6.5 DelayedArray_0.2.7 matrixStats_0.53.1   
  Biobase_2.36.2
[17] BiocParallel_1.10.1Rsamtools_1.28.0   Biostrings_2.44.2
  XVector_0.16.0
[21] GenomicRanges_1.28.6   GenomeInfoDb_1.12.2IRanges_2.10.4   
  S4Vectors_0.14.6  
[25] BiocGenerics_0.22.0   

loaded via a namespace (and not attached):
  [1] backports_1.1.2   GOstats_2.42.0Hmisc_4.1-1   
   
  [4] AnnotationHub_2.8.2   LSD_4.0-0 plyr_1.8.4
   
  [7] lazyeval_0.2.1GSEABase_1.38.2   splines_3.4.0 
   
 [10] BatchJobs_1.7 easyRNASeq_2.12.1 digest_0.6.15 
   
 [13] BiocInstaller_1.28.0  ensembldb_2.0.4   
htmltools_0.3.6  
 [16] GO.db_3.4.1   gdata_2.18.0  magrittr_1.5  
   
 [19] checkmate_1.8.5   memoise_1.1.0 BBmisc_1.11   
   
 [22] BSgenome_1.44.2   cluster_2.0.6 DEXSeq_1.22.0 
   
 [25] limma_3.32.7  annotate_1.54.0   
colorspace_1.3-2 
 [28] blob_1.1.0RCurl_1.95-4.10   graph_1.54.0  
   
 [31] genefilter_1.58.1 brew_1.0-6
survival_2.41-3  
 [34] sendmailR_1.2-1   VariantAnnotation_1.22.3  ape_5.0   
   
 [37] gtable_0.2.0  zlibbioc_1.22.0   scales_0.5.0  
   
 [40] DESeq_1.28.0  pheatmap_1.0.8vsn_3.44.0
   
 [43] DBI_0.7   edgeR_3.18.1  Rcpp_0.12.15  
   
 [46] xtable_1.8-2  htmlTable_1.11.2  
foreign_0.8-69   
 [49] bit_1.1-12preprocessCore_1.38.1 Formula_1.2-2 
   
 [52] intervals_0.15.1  AnnotationForge_1.18.2getopt_1.20.1 
   
 [55] htmlwidgets_0.9   httr_1.3.1gplots_3.0.1  
   
 [58] RColorBrewer_1.1-2acepack_1.4.1 
pkgconfig_2.0.1  
 [61] reshape_0.8.7 XML_3.98-1.9  Gviz_1.20.0   
   
 [64] nnet_7.3-12   locfit_1.5-9.1rlang_0.1.6   
   
 [67] reshape2_1.4.3munsell_0.4.3 tools_3.4.0   
   
 [70] qrqc_1.30.0   RSQLite_2.0   
evaluate_0.10.1  
 [73] stringr_1.2.0 yaml_2.1.16   bit64_0.9-7   
   
 [76] caTools_1.17.1AnnotationFilter_1.0.0