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plantarum / flowPloidy

An R package for flow cytometry histogram analysis
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issue with installation #3

Closed alex-rapp closed 4 years ago

alex-rapp commented 4 years ago

after following the installation procedure (stable) I get the following error when I try to load the library: Error: package or namespace load failed for ‘flowPloidy’ in rbind(info, getNamespaceInfo(env, "S3methods")): number of columns of matrices must match (see arg 2)

I tried to remove and reinstall the package without any change. Thanks for your help. Alex

plantarum commented 4 years ago

Hi Alex,

Thanks for your interest!

I will need more info to figure out what's going on here. Can you tell me:

Thanks,

Tyler

alex-rapp writes:

after following the installation procedure (stable) I get the following error when I try to load the library: Error: package or namespace load failed for ‘flowPloidy’ in rbind(info, getNamespaceInfo(env, "S3methods")): number of columns of matrices must match (see arg 2)

I tried to remove and reinstall the package without any change. Thanks for your help. Alex

-- Tyler Smith plantarum.ca

alex-rapp commented 4 years ago

Hi Tylor, Thanks for the quick answer. Here are my details:

MacOS 10.14.6

R: platform x86_64-apple-darwin15.6.0
arch x86_64
os darwin15.6.0
system x86_64, darwin15.6.0
status
major 3
minor 5.2
year 2018
month 12
day 20
svn rev 75870
language R
version.string R version 3.5.2 (2018-12-20) nickname Eggshell Igloo

Bioconductor: 3.8

I first tried to install flowPloidy from bioconductor with the above mentioned error. Then I tried using the Devtool variant, together with GitHub. I updated all the dependencies, had some trouble with pdftools and sm, required a manual download and installation from the tar file for them. Still encountered the above mentioned error. After some googling found some hints that the installation might be broken, so I then deinstalled flowPloidy and reinstalled it. Installation went through without any problem, but still the error occurs when I try to load the library: library(flowPloidy) Error: package or namespace load failed for ‘flowPloidy’ in rbind(info, getNamespaceInfo(env, "S3methods")): number of columns of matrices must match (see arg 2)

Btw. flowPloidyData loads without problems. And I just realised that flowPloidy is not listed in the list of available packages (see attached image), although the installation process was fine.

Thanks a lot for your help, best wishes Alex

On 4. Jun 2020, at 21:39, Tyler Smith notifications@github.com wrote:

Hi Alex,

Thanks for your interest!

I will need more info to figure out what's going on here. Can you tell me:

  • Your OS (Windows, Mac, Linux; and version/release)

  • Your R version

  • Your Bioconductor version

  • How you are installing flowPloidy (from github via devtoos, or from bioconductor?)

Thanks,

Tyler

alex-rapp writes:

after following the installation procedure (stable) I get the following error when I try to load the library: Error: package or namespace load failed for ‘flowPloidy’ in rbind(info, getNamespaceInfo(env, "S3methods")): number of columns of matrices must match (see arg 2)

I tried to remove and reinstall the package without any change. Thanks for your help. Alex

-- Tyler Smith plantarum.ca — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/plantarum/flowPloidy/issues/3#issuecomment-639073947, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJXHM7DP375QHK336RXRQE3RU7Z6TANCNFSM4NS2CPCA.

plantarum commented 4 years ago

Hi Alex,

I've just reinstalled flowPloidy on a recently-installed R 4.0, and it went off without a problem. The kind of error you're describing sounds more like a mismatch of library versions, rather than a problem with the package itself.

The easiest thing to try is probably upgrading your R installation to 4.0, since 3.5 is two years old now. The Bioconductor system targets the very latest R version, and that may be where our problem is coming from.

If you are unable to upgrade R, I'll have to do some deeper digging.

Best,

Tyler

alex-rapp writes:

Hi Tylor, Thanks for the quick answer. Here are my details:

MacOS 10.14.6

R: platform x86_64-apple-darwin15.6.0
arch x86_64
os darwin15.6.0
system x86_64, darwin15.6.0
status
major 3
minor 5.2
year 2018
month 12
day 20
svn rev 75870
language R
version.string R version 3.5.2 (2018-12-20) nickname Eggshell Igloo

Bioconductor: 3.8

I first tried to install flowPloidy from bioconductor with the above mentioned error. Then I tried using the Devtool variant, together with GitHub. I updated all the dependencies, had some trouble with pdftools and sm, required a manual download and installation from the tar file for them. Still encountered the above mentioned error. After some googling found some hints that the installation might be broken, so I then deinstalled flowPloidy and reinstalled it. Installation went through without any problem, but still the error occurs when I try to load the library: library(flowPloidy) Error: package or namespace load failed for ‘flowPloidy’ in rbind(info, getNamespaceInfo(env, "S3methods")): number of columns of matrices must match (see arg 2)

Btw. flowPloidyData loads without problems. And I just realised that flowPloidy is not listed in the list of available packages (see attached image), although the installation process was fine.

Thanks a lot for your help, best wishes Alex

On 4. Jun 2020, at 21:39, Tyler Smith notifications@github.com wrote:

Hi Alex,

Thanks for your interest!

I will need more info to figure out what's going on here. Can you tell me:

  • Your OS (Windows, Mac, Linux; and version/release)

  • Your R version

  • Your Bioconductor version

  • How you are installing flowPloidy (from github via devtoos, or from bioconductor?)

Thanks,

Tyler

alex-rapp writes:

after following the installation procedure (stable) I get the following error when I try to load the library: Error: package or namespace load failed for ‘flowPloidy’ in rbind(info, getNamespaceInfo(env, "S3methods")): number of columns of matrices must match (see arg 2)

I tried to remove and reinstall the package without any change. Thanks for your help. Alex

-- Tyler Smith plantarum.ca — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/plantarum/flowPloidy/issues/3#issuecomment-639073947, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJXHM7DP375QHK336RXRQE3RU7Z6TANCNFSM4NS2CPCA.

-- Tyler Smith plantarum.ca

alex-rapp commented 4 years ago

Hi Tyler, Thanks for the answer, I will give it a try tomorrow with a fresh install in version 4. I’ll keep you updated. Thanks Alex

On 8. Jun 2020, at 21:15, Tyler Smith notifications@github.com wrote:

Hi Alex,

I've just reinstalled flowPloidy on a recently-installed R 4.0, and it went off without a problem. The kind of error you're describing sounds more like a mismatch of library versions, rather than a problem with the package itself.

The easiest thing to try is probably upgrading your R installation to 4.0, since 3.5 is two years old now. The Bioconductor system targets the very latest R version, and that may be where our problem is coming from.

If you are unable to upgrade R, I'll have to do some deeper digging.

Best,

Tyler

alex-rapp writes:

Hi Tylor, Thanks for the quick answer. Here are my details:

MacOS 10.14.6

R: platform x86_64-apple-darwin15.6.0 arch x86_64 os darwin15.6.0 system x86_64, darwin15.6.0 status major 3 minor 5.2 year 2018 month 12 day 20 svn rev 75870 language R version.string R version 3.5.2 (2018-12-20) nickname Eggshell Igloo

Bioconductor: 3.8

I first tried to install flowPloidy from bioconductor with the above mentioned error. Then I tried using the Devtool variant, together with GitHub. I updated all the dependencies, had some trouble with pdftools and sm, required a manual download and installation from the tar file for them. Still encountered the above mentioned error. After some googling found some hints that the installation might be broken, so I then deinstalled flowPloidy and reinstalled it. Installation went through without any problem, but still the error occurs when I try to load the library: library(flowPloidy) Error: package or namespace load failed for ‘flowPloidy’ in rbind(info, getNamespaceInfo(env, "S3methods")): number of columns of matrices must match (see arg 2)

Btw. flowPloidyData loads without problems. And I just realised that flowPloidy is not listed in the list of available packages (see attached image), although the installation process was fine.

Thanks a lot for your help, best wishes Alex

On 4. Jun 2020, at 21:39, Tyler Smith notifications@github.com wrote:

Hi Alex,

Thanks for your interest!

I will need more info to figure out what's going on here. Can you tell me:

  • Your OS (Windows, Mac, Linux; and version/release)

  • Your R version

  • Your Bioconductor version

  • How you are installing flowPloidy (from github via devtoos, or from bioconductor?)

Thanks,

Tyler

alex-rapp writes:

after following the installation procedure (stable) I get the following error when I try to load the library: Error: package or namespace load failed for ‘flowPloidy’ in rbind(info, getNamespaceInfo(env, "S3methods")): number of columns of matrices must match (see arg 2)

I tried to remove and reinstall the package without any change. Thanks for your help. Alex

-- Tyler Smith plantarum.ca — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/plantarum/flowPloidy/issues/3#issuecomment-639073947, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJXHM7DP375QHK336RXRQE3RU7Z6TANCNFSM4NS2CPCA.

-- Tyler Smith plantarum.ca — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/plantarum/flowPloidy/issues/3#issuecomment-640819539, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJXHM7HLRQTGALD4LU25LI3RVU2EHANCNFSM4NS2CPCA.

alex-rapp commented 4 years ago

Hi Tyler, I managed to get flowPloidy installed. On two of my other machines it went without a problem. Both with a rather old (R3.5) and a brand new (R4, Win10) machine, I managed to install the stable release as you described in your manual. Sorry for having you bothered, best wishes Alex

On 8. Jun 2020, at 21:15, Tyler Smith notifications@github.com wrote:

Hi Alex,

I've just reinstalled flowPloidy on a recently-installed R 4.0, and it went off without a problem. The kind of error you're describing sounds more like a mismatch of library versions, rather than a problem with the package itself.

The easiest thing to try is probably upgrading your R installation to 4.0, since 3.5 is two years old now. The Bioconductor system targets the very latest R version, and that may be where our problem is coming from.

If you are unable to upgrade R, I'll have to do some deeper digging.

Best,

Tyler

alex-rapp writes:

Hi Tylor, Thanks for the quick answer. Here are my details:

MacOS 10.14.6

R: platform x86_64-apple-darwin15.6.0 arch x86_64 os darwin15.6.0 system x86_64, darwin15.6.0 status major 3 minor 5.2 year 2018 month 12 day 20 svn rev 75870 language R version.string R version 3.5.2 (2018-12-20) nickname Eggshell Igloo

Bioconductor: 3.8

I first tried to install flowPloidy from bioconductor with the above mentioned error. Then I tried using the Devtool variant, together with GitHub. I updated all the dependencies, had some trouble with pdftools and sm, required a manual download and installation from the tar file for them. Still encountered the above mentioned error. After some googling found some hints that the installation might be broken, so I then deinstalled flowPloidy and reinstalled it. Installation went through without any problem, but still the error occurs when I try to load the library: library(flowPloidy) Error: package or namespace load failed for ‘flowPloidy’ in rbind(info, getNamespaceInfo(env, "S3methods")): number of columns of matrices must match (see arg 2)

Btw. flowPloidyData loads without problems. And I just realised that flowPloidy is not listed in the list of available packages (see attached image), although the installation process was fine.

Thanks a lot for your help, best wishes Alex

On 4. Jun 2020, at 21:39, Tyler Smith notifications@github.com wrote:

Hi Alex,

Thanks for your interest!

I will need more info to figure out what's going on here. Can you tell me:

  • Your OS (Windows, Mac, Linux; and version/release)

  • Your R version

  • Your Bioconductor version

  • How you are installing flowPloidy (from github via devtoos, or from bioconductor?)

Thanks,

Tyler

alex-rapp writes:

after following the installation procedure (stable) I get the following error when I try to load the library: Error: package or namespace load failed for ‘flowPloidy’ in rbind(info, getNamespaceInfo(env, "S3methods")): number of columns of matrices must match (see arg 2)

I tried to remove and reinstall the package without any change. Thanks for your help. Alex

-- Tyler Smith plantarum.ca — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/plantarum/flowPloidy/issues/3#issuecomment-639073947, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJXHM7DP375QHK336RXRQE3RU7Z6TANCNFSM4NS2CPCA.

-- Tyler Smith plantarum.ca — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/plantarum/flowPloidy/issues/3#issuecomment-640819539, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJXHM7HLRQTGALD4LU25LI3RVU2EHANCNFSM4NS2CPCA.

plantarum commented 4 years ago

No problem Alex, I'm glad it's working now! Version conflicts like this can be tricky to detect and resolve.