[R-pkg-devel] Packages required and available but unsuitable versions: Error

[Agarwal, Divyansh]

Dear R developers community,

I’m trying to build and submit an R package to CRAN but keep getting the 
following error:
Packages required and available but unsuitable versions:
  'org.Hs.eg.db', 'org.Mm.eg.db', 'org.Ce.eg.db'

The DESCRIPTION file for my package includes the following:
Depends:
  R (>= 3.5.0),
  stats (>= 3.5.0),
  MASS (>= 7.3-49),
Encoding: UTF-8
Imports:
  nbpMatching (>= 1.5.1),
  crossmatch (>= 1.3-1),
  Matrix (>= 1.2-17),
  org.Hs.eg.db (>= 3.6.0),
  org.Mm.eg.db (>= 3.6.0),
  org.Ce.eg.db (>= 3.6.0),
  Seurat (>= 3.0.0),
  AnnotationDbi (>= 1.42.1)

The details of the error log are here: 


I’ve tried a few different things such as specifying an R version under 
“Depends” or updating the version for the “org.” packages to the latest version 
(>=3.8) but I haven’t been able to resolve the error and warnings shown in the 
error log.  I would be really grateful to you if you could kindly advise a 
potential solution for how to possibly fix this error.

Thanks a lot in advance!
Divyansh



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Re: [R-pkg-devel] Packages required and available but unsuitable versions: Error

[Martin Morgan]

Probably the easiest 'solution' is to remove the version dependencies, e.g., 
'org.Hs.eg.db, org.Mm.eg.db, ...'.

I suspect that the root cause is that the Windows builders do not have the 
correct version of these packages installed for the version of R in use, 
perhaps because the version of the package BiocVersion (it should be 3.10.1 in 
R-devel) is incorrect.

Martin Morgan
Bioconductor

On 9/23/19, 6:06 AM, "R-package-devel on behalf of Agarwal, Divyansh" 
 wrote:

Dear R developers community,

I’m trying to build and submit an R package to CRAN but keep getting the 
following error:
Packages required and available but unsuitable versions:
  'org.Hs.eg.db', 'org.Mm.eg.db', 'org.Ce.eg.db'

The DESCRIPTION file for my package includes the following:
Depends:
  R (>= 3.5.0),
  stats (>= 3.5.0),
  MASS (>= 7.3-49),
Encoding: UTF-8
Imports:
  nbpMatching (>= 1.5.1),
  crossmatch (>= 1.3-1),
  Matrix (>= 1.2-17),
  org.Hs.eg.db (>= 3.6.0),
  org.Mm.eg.db (>= 3.6.0),
  org.Ce.eg.db (>= 3.6.0),
  Seurat (>= 3.0.0),
  AnnotationDbi (>= 1.42.1)

The details of the error log are here: 


I’ve tried a few different things such as specifying an R version under 
“Depends” or updating the version for the “org.” packages to the latest version 
(>=3.8) but I haven’t been able to resolve the error and warnings shown in the 
error log.  I would be really grateful to you if you could kindly advise a 
potential solution for how to possibly fix this error.

Thanks a lot in advance!
Divyansh



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Re: [R-pkg-devel] [External] Re: Packages required and available but unsuitable versions: Error

[Agarwal, Divyansh]

Hi Martin,

Thanks so much. Removing the version dependencies for those 3 packages fixed 
the ERROR but I'm now having an issue with these WARNINGS:
Warning: replacing previous import ‘AnnotationDbi::select’ by ‘MASS::select’ 
when loading ‘multicross’
Warning: replacing previous import ‘Matrix::cov2cor’ by ‘stats::cov2cor’ when 
loading ‘multicross’
Warning: replacing previous import ‘Matrix::toeplitz’ by ‘stats::toeplitz’ when 
loading ‘multicross’
Warning: replacing previous import ‘nbpMatching::quantile’ by ‘stats::quantile’ 
when loading ‘multicross’
Warning: replacing previous import ‘Matrix::update’ by ‘stats::update’ when 
loading ‘multicross’

Looking at a couple of forums I thought putting stats and MASS under "Depends" 
in the DESCRIPTION file would address these warnings, but they still come up. 
For reference, my DESCRIPTION file is –

Depends:
  stats (>= 3.5.0),
  MASS (>= 7.3-49),
Encoding: UTF-8
 Imports:
  nbpMatching (>= 1.5.1),
  crossmatch (>= 1.3-1),
  Matrix (>= 1.2-17),
  org.Hs.eg.db (>= 3.6.0),
  org.Mm.eg.db (>= 3.6.0),
  org.Ce.eg.db (>= 3.6.0),
  Seurat (>= 3.0.0),
  AnnotationDbi (>= 1.42.1)

Please let me know what you'd recommend. Thank you again for taking the time to 
offer your help, and am really grateful for your suggestions. 

Sincerely,
Divyansh


On 9/23/19, 7:44 AM, "Martin Morgan"  wrote:

Probably the easiest 'solution' is to remove the version dependencies, 
e.g., 'org.Hs.eg.db, org.Mm.eg.db, ...'.

I suspect that the root cause is that the Windows builders do not have the 
correct version of these packages installed for the version of R in use, 
perhaps because the version of the package BiocVersion (it should be 3.10.1 in 
R-devel) is incorrect.

Martin Morgan
Bioconductor

On 9/23/19, 6:06 AM, "R-package-devel on behalf of Agarwal, Divyansh" 
 wrote:

Dear R developers community,

I’m trying to build and submit an R package to CRAN but keep getting 
the following error:
Packages required and available but unsuitable versions:
  'org.Hs.eg.db', 'org.Mm.eg.db', 'org.Ce.eg.db'

The DESCRIPTION file for my package includes the following:
Depends:
  R (>= 3.5.0),
  stats (>= 3.5.0),
  MASS (>= 7.3-49),
Encoding: UTF-8
Imports:
  nbpMatching (>= 1.5.1),
  crossmatch (>= 1.3-1),
  Matrix (>= 1.2-17),
  org.Hs.eg.db (>= 3.6.0),
  org.Mm.eg.db (>= 3.6.0),
  org.Ce.eg.db (>= 3.6.0),
  Seurat (>= 3.0.0),
  AnnotationDbi (>= 1.42.1)

The details of the error log are here: 


I’ve tried a few different things such as specifying an R version under 
“Depends” or updating the version for the “org.” packages to the latest version 
(>=3.8) but I haven’t been able to resolve the error and warnings shown in the 
error log.  I would be really grateful to you if you could kindly advise a 
potential solution for how to possibly fix this error.

Thanks a lot in advance!
Divyansh



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R-package-devel@r-project.org mailing list
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Re: [R-pkg-devel] [External] Re: Packages required and available but unsuitable versions: Error

[Martin Morgan]

The warnings are fixed by changing the NAMESPACE file, not the DESCRIPTION 
file. Decide which function(s) you would like to import, and import only those 
using importFrom("Matrix", "sparseMatrix") or import("Matrix", except = 
"toeplitz")

Martin

On 9/23/19, 8:45 AM, "Agarwal, Divyansh" 
 wrote:

Hi Martin,

Thanks so much. Removing the version dependencies for those 3 packages 
fixed the ERROR but I'm now having an issue with these WARNINGS:
Warning: replacing previous import ‘AnnotationDbi::select’ by 
‘MASS::select’ when loading ‘multicross’
Warning: replacing previous import ‘Matrix::cov2cor’ by ‘stats::cov2cor’ 
when loading ‘multicross’
Warning: replacing previous import ‘Matrix::toeplitz’ by ‘stats::toeplitz’ 
when loading ‘multicross’
Warning: replacing previous import ‘nbpMatching::quantile’ by 
‘stats::quantile’ when loading ‘multicross’
Warning: replacing previous import ‘Matrix::update’ by ‘stats::update’ when 
loading ‘multicross’

Looking at a couple of forums I thought putting stats and MASS under 
"Depends" in the DESCRIPTION file would address these warnings, but they still 
come up. For reference, my DESCRIPTION file is –

Depends:
  stats (>= 3.5.0),
  MASS (>= 7.3-49),
Encoding: UTF-8
 Imports:
  nbpMatching (>= 1.5.1),
  crossmatch (>= 1.3-1),
  Matrix (>= 1.2-17),
  org.Hs.eg.db (>= 3.6.0),
  org.Mm.eg.db (>= 3.6.0),
  org.Ce.eg.db (>= 3.6.0),
  Seurat (>= 3.0.0),
  AnnotationDbi (>= 1.42.1)

Please let me know what you'd recommend. Thank you again for taking the 
time to offer your help, and am really grateful for your suggestions. 

Sincerely,
Divyansh


On 9/23/19, 7:44 AM, "Martin Morgan"  wrote:

Probably the easiest 'solution' is to remove the version dependencies, 
e.g., 'org.Hs.eg.db, org.Mm.eg.db, ...'.

I suspect that the root cause is that the Windows builders do not have 
the correct version of these packages installed for the version of R in use, 
perhaps because the version of the package BiocVersion (it should be 3.10.1 in 
R-devel) is incorrect.

Martin Morgan
Bioconductor

On 9/23/19, 6:06 AM, "R-package-devel on behalf of Agarwal, Divyansh" 
 wrote:

Dear R developers community,

I’m trying to build and submit an R package to CRAN but keep 
getting the following error:
Packages required and available but unsuitable versions:
  'org.Hs.eg.db', 'org.Mm.eg.db', 'org.Ce.eg.db'

The DESCRIPTION file for my package includes the following:
Depends:
  R (>= 3.5.0),
  stats (>= 3.5.0),
  MASS (>= 7.3-49),
Encoding: UTF-8
Imports:
  nbpMatching (>= 1.5.1),
  crossmatch (>= 1.3-1),
  Matrix (>= 1.2-17),
  org.Hs.eg.db (>= 3.6.0),
  org.Mm.eg.db (>= 3.6.0),
  org.Ce.eg.db (>= 3.6.0),
  Seurat (>= 3.0.0),
  AnnotationDbi (>= 1.42.1)

The details of the error log are here: 


I’ve tried a few different things such as specifying an R version 
under “Depends” or updating the version for the “org.” packages to the latest 
version (>=3.8) but I haven’t been able to resolve the error and warnings shown 
in the error log.  I would be really grateful to you if you could kindly advise 
a potential solution for how to possibly fix this error.

Thanks a lot in advance!
Divyansh



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[R-pkg-devel] unicode WARNING on solaris?

[Toby Hocking]

Hi all,

is there a known fix for this WARNING which I am getting on solaris for my
newly submitted nc package?
https://www.r-project.org/nosvn/R.check/r-patched-solaris-x86/nc-00check.html

A quick google search for "it is not known that wchar_t is Unicode on this
platform cran" shows that many other packages have this WARNING as well.

I searched r-devel and r-pkg-devel for the warning text but I did not find
any messages discussing a fix.

Thanks for any help
Toby

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