Balasubramanian Narasimhan
| Snapshot Date: 2024-11-27 13:40 -0500 (Wed, 27 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/impute |
| git_branch: devel |
| git_last_commit: bd0db5e |
| git_last_commit_date: 2024-10-29 09:22:27 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-11-28 12:17 -0500 (Thu, 28 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4748 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4459 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4398 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1017/2272 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| impute 1.81.0 (landing page) Balasubramanian Narasimhan
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
|
To the developers/maintainers of the impute package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/impute.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: impute |
| Version: 1.81.0 |
| Command: rm -rf impute.buildbin-libdir && mkdir impute.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh impute_1.81.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R impute.buildbin-libdir |
| StartedAt: 2024-11-28 04:06:07 -0500 (Thu, 28 Nov 2024) |
| EndedAt: 2024-11-28 04:06:20 -0500 (Thu, 28 Nov 2024) |
| EllapsedTime: 12.6 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: impute_1.81.0.tgz |
| PackageFileSize: 646 KiB |
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### Running command:
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### rm -rf impute.buildbin-libdir && mkdir impute.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh impute_1.81.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R impute.buildbin-libdir
###
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=impute.buildbin-libdir impute_1.81.0.tar.gz'
>>>>>>>
* installing *source* package ‘impute’ ...
** using staged installation
** libs
using Fortran compiler: ‘GNU Fortran (GCC) 12.2.0’
using SDK: ‘MacOSX11.3.sdk’
/opt/gfortran/bin/gfortran -arch x86_64 -fPIC -Wall -g -O2 -c knnimpute.f -o knnimpute.o
f951: Warning: Nonconforming tab character in column 1 of line 89 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 91 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 92 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 93 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 94 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 95 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 96 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 97 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 98 [-Wtabs]
f951: Warning: Nonconforming tab character in column 3 of line 99 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 100 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 101 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 102 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 103 [-Wtabs]
f951: Warning: Nonconforming tab character in column 3 of line 104 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 105 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 106 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 107 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 108 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 109 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 110 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 111 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 112 [-Wtabs]
f951: Warning: Nonconforming tab character in column 3 of line 113 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 114 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 115 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 116 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 117 [-Wtabs]
f951: Warning: Nonconforming tab character in column 3 of line 118 [-Wtabs]
f951: Warning: Nonconforming tab character in column 3 of line 119 [-Wtabs]
f951: Warning: Nonconforming tab character in column 3 of line 120 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 121 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 122 [-Wtabs]
knnimpute.f:99:72:
99 | 20 pos(k1+1) = pos(k1)
| 1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 20 at (1)
knnimpute.f:113:72:
113 | 35 pos(k1+1) = pos(k1)
| 1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 35 at (1)
knnimpute.f:168:72:
168 | ratio=dabs(dnew-dold)/dold
| ^
Warning: ‘dold’ may be used uninitialized [-Wmaybe-uninitialized]
knnimpute.f:132:33:
132 | double precision ratio,dold,dnew
| ^
note: ‘dold’ was declared here
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o impute.so knnimpute.o -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.21-bioc/meat/impute.buildbin-libdir/00LOCK-impute/00new/impute/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (impute)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR impute.buildbin-libdir/impute/libs/impute.so
>>>>>>>
>>>>>>> Paths before fix:
impute.buildbin-libdir/impute/libs/impute.so:
impute.so (compatibility version 0.0.0, current version 0.0.0)
/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgcc_s.1.1.dylib" "impute.buildbin-libdir/impute/libs/impute.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgfortran.5.dylib" "impute.buildbin-libdir/impute/libs/impute.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libquadmath.0.dylib" "impute.buildbin-libdir/impute/libs/impute.so"
install_name_tool -change "/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgfortran.5.dylib" "impute.buildbin-libdir/impute/libs/impute.so"
install_name_tool -change "/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libquadmath.0.dylib" "impute.buildbin-libdir/impute/libs/impute.so"
>>>>>>> Paths after fix:
impute.buildbin-libdir/impute/libs/impute.so:
impute.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)