‘imageListToMatrix’ is not exported by 'namespace:ANTsRCore'

[avalcarcel9]

Updated the package and now it won't load due to a potential namespace conflict.

source("https://neuroconductor.org/neurocLite.R") Bioconductor version 3.7 (BiocInstaller 1.29.6), ?biocLite for help A newer version of Bioconductor is available for this version of R, ?BiocUpgrade for help BioC_mirror: https://bioconductor.org Using Bioconductor 3.7 (BiocInstaller 1.29.6), R 3.5.0 (2018-04-23). Using neurocLite version: # neurocInstall package version: 0.11.0 neuro_install('extrantsr') trying URL 'https://neuroconductor.org/releases/2018/Sep/bin/macosx/el-capitan/contrib/3.5/extrantsr_3.9.1.9000.tgz' Content type 'application/x-gtar' length 550500 bytes (537 KB)

downloaded 537 KB

The downloaded binary packages are in /var/folders/sq/x3htb34928bfn79jk3qksqg56zmf39/T//RtmpkCTHN8/downloaded_packages

library(extrantsr) Error: package or namespace load failed for ‘extrantsr’: object ‘imageListToMatrix’ is not exported by 'namespace:ANTsRCore'

[muschellij2]

Please print your info for ANTsRCore, you need >= 0.6.3 for this version of extrantsr.

Try again with neuroc_install("extrantsr", upgrade_dependencies = TRUE) John

On Fri, Jan 4, 2019 at 7:13 PM Alessandra Valcarcel < notifications@github.com> wrote:

Updated the package and now it won't load due to a potential namespace conflict.

source("https://neuroconductor.org/neurocLite.R") Bioconductor version 3.7 (BiocInstaller 1.29.6), ?biocLite for help A newer version of Bioconductor is available for this version of R, ?BiocUpgrade for help BioC_mirror: https://bioconductor.org Using Bioconductor 3.7 (BiocInstaller 1.29.6), R 3.5.0 (2018-04-23). Using neurocLite version: # neurocInstall package version: 0.11.0 neuro_install('extrantsr') trying URL ' https://neuroconductor.org/releases/2018/Sep/bin/macosx/el-capitan/contrib/3.5/extrantsr_3.9.1.9000.tgz ' Content type 'application/x-gtar' length 550500 bytes (537 KB)

downloaded 537 KB

The downloaded binary packages are in

/var/folders/sq/x3htb34928bfn79jk3qksqg56zmf39/T//RtmpkCTHN8/downloaded_packages

library(extrantsr) Error: package or namespace load failed for ‘extrantsr’: object ‘imageListToMatrix’ is not exported by 'namespace:ANTsRCore'

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[avalcarcel9]

I was using 0.5.7.2 but did try it with upgrade_dependencies = TRUE and it still failed. I'll manually update ANTsRCore and hopefully that fixes the issue.

[avalcarcel9]

Tried to update ANTsRCore using neuroconductor

neuro_install('ANTsRCore', release = "current", release_repo = "github", upgrade_dependencies = TRUE) Downloading GitHub repo neuroconductor/ANTsRCore@4cda7da5fe1e70591b8af1b85062c4fb985fbeff These packages have more recent versions available. Which would you like to update?

1: ITKR (be7777c7c... -> eb4b623ab...) [GitHub]

Enter one or more numbers separated by spaces, or an empty line to cancel 1: ✔ checking for file ‘/private/var/folders/sq/x3htb34928bfn79jk3qksqg56zmf39/T/RtmpnyNsDp/remotesb63579cd686/neuroconductor-ANTsRCore-4cda7da/DESCRIPTION’ ... ─ preparing ‘ANTsRCore’: ✔ checking DESCRIPTION meta-information ... ─ cleaning src ─ running ‘cleanup’ ─ checking for LF line-endings in source and make files and shell scripts ─ checking for empty or unneeded directories ─ looking to see if a ‘data/datalist’ file should be added ─ building ‘ANTsRCore_0.6.3.tar.gz’ Warning: invalid uid value replaced by that for user 'nobody' Warning: invalid gid value replaced by that for user 'nobody'

ERROR: failed to lock directory ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ for modifying Try removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/00LOCK-ANTsRCore’ Show Traceback

Rerun with Debug Error in i.p(...) : (converted from warning) installation of package ‘/var/folders/sq/x3htb34928bfn79jk3qksqg56zmf39/T//RtmpnyNsDp/fileb63526054fb1/ANTsRCore_0.6.3.tar.gz’ had non-zero exit status

Manually updated ITKR and the error remained the same. Is this related? Is there another way to download ANTsRCore >= 0.6.3 besides the current neuroconductor version?

[muschellij2]

Try removing ‘/Library/Frameworks/R.framework/Versions/3.5/ Resources/library/00LOCK-

On Fri, Jan 4, 2019 at 10:38 PM Alessandra Valcarcel < notifications@github.com> wrote:

Tried to update ANTsRCore using neuroconductor

neuro_install('ANTsRCore', release = "current", release_repo = "github", upgrade_dependencies = TRUE) Downloading GitHub repo neuroconductor/ANTsRCore@4cda7da https://github.com/neuroconductor/ANTsRCore/commit/4cda7da5fe1e70591b8af1b85062c4fb985fbeff These packages have more recent versions available. Which would you like to update?

1: ITKR (be7777c7c... -> eb4b623ab...) [GitHub]

Enter one or more numbers separated by spaces, or an empty line to cancel 1: ✔ checking for file ‘/private/var/folders/sq/x3htb34928bfn79jk3qksqg56zmf39/T/RtmpnyNsDp/remotesb63579cd686/neuroconductor-ANTsRCore-4cda7da/DESCRIPTION’ ... ─ preparing ‘ANTsRCore’: ✔ checking DESCRIPTION meta-information ... ─ cleaning src ─ running ‘cleanup’ ─ checking for LF line-endings in source and make files and shell scripts ─ checking for empty or unneeded directories ─ looking to see if a ‘data/datalist’ file should be added ─ building ‘ANTsRCore_0.6.3.tar.gz’ Warning: invalid uid value replaced by that for user 'nobody' Warning: invalid gid value replaced by that for user 'nobody'

ERROR: failed to lock directory ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ for modifying Try removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/00LOCK-ANTsRCore’ Show Traceback

Rerun with Debug Error in i.p(...) : (converted from warning) installation of package ‘/var/folders/sq/x3htb34928bfn79jk3qksqg56zmf39/T//RtmpnyNsDp/fileb63526054fb1/ANTsRCore_0.6.3.tar.gz’ had non-zero exit status

Manually updated ITKR and the error remained the same. Is this related? Is there another way to download ANTsRCore >= 0.6.3 besides the current neuroconductor version?

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-- John

[avalcarcel9]

That worked. Thanks for the help!