Cannot load library multtest; package or namespace load failed
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Entering edit mode
Guido Hooiveld ★ 4.0k
@guido-hooiveld-2020
Last seen 6 hours ago
Wageningen University, Wageningen, the …

After upgrading to BioC 3.4 it turns out I cannot load the library multtest anymore. Uninstalling followed by reinstalling, even from source, does not solve it. Is this something specific to my system, or a more general error?

Thanks, Guido

> library(multtest)
<<snip>>

Error in namespaceExport(ns, exports) :
  undefined exports: Surv, aareg, agreg.fit, agexact.fit, attrassign, basehaz, cch, clogit, cluster, cox.zph, coxph, coxph.control, coxph.detail, coxph.fit, coxph.wtest, finegray, format.Surv, frailty, frailty.gamma, frailty.gaussian, frailty.t, is.Surv, is.na.Surv, is.ratetable, labels.survreg, match.ratetable, neardate, psurvreg, qsurvreg, dsurvreg, pspline, pyears, ratetable, ratetableDate, ridge, rsurvreg, statefig, strata, survConcordance, survSplit, survdiff, survexp, survfit, survfit.formula, survfitcoxph.fit, survfitKM, survfitCI, survobrien, survpenal.fit, survConcordance.fit, survreg, survreg.control, survreg.fit, survreg.distributions, survregDtest, tcut, tmerge, untangle.specials
In addition: Warning message:
S3 methods ‘[.aareg’, ‘[.Surv’, ‘[.cox.zph’, ‘[.coxph.penalty’, ‘[.ratetable’, ‘[.ratetable2’, ‘[.survfit’, ‘[.survfitms’, ‘[.tcut’, ‘Math.Surv’, ‘Math.ratetable’, ‘Ops.Surv’, ‘Ops.ratetable’, ‘Summary.Surv’, ‘anova.coxph’, ‘anova.coxphlist’, ‘anova.survreg’, ‘anova.survreglist’, ‘as.character.Surv’, ‘as.data.frame.Surv’, ‘as.matrix.ratetable’, ‘as.matrix.Surv’, ‘attrassign.default’, ‘attrassign.lm’, ‘extractAIC.coxph.penal’, ‘dim.survfit’, ‘dim.survfitms’, ‘format.Surv’, ‘is.na.Surv’, ‘is.na.coxph.penalty’, ‘is.na.ratetable’, ‘labels.survreg’, ‘levels.tcut’, ‘lines.aareg’, ‘lines.survexp’, ‘lines.survfit’, ‘logLik.coxph’, ‘logLik.survreg’, ‘makepredictcall.pspline’, ‘model.frame.coxph’, ‘model.frame.survreg’, ‘model.matrix.coxph’, ‘model.matrix.survreg’, ‘plot.aareg’, ‘plot.cox.zph’, ‘plot.survfit’, ‘points.survfit’, ‘predict.coxph’, ‘predict.coxph.penal’, ‘predict.pspline’, ‘predict.survreg’, ‘predict.survreg.penal’, ‘print.Surv’, ‘print.aareg’, ‘print.cch’, ‘print.clogit’, ‘print.co [... truncated]
Error: package or namespace load failed for ‘multtest’
>
>
>  remove.packages("multtest")
Removing package from ‘C:/Program Files/R/R-3.3.1patched/library’
(as ‘lib’ is unspecified)
> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
> biocLite("multtest")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.1 Patched (2016-10-18
  r71535).
Installing package(s) ‘multtest’
trying URL 'https://bioconductor.org/packages/3.4/bioc/bin/windows/contrib/3.3/multtest_2.30.0.zip'
Content type 'application/zip' length 1359546 bytes (1.3 MB)
downloaded 1.3 MB

package ‘multtest’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        D:\TMP\RtmpcrIJn3\downloaded_packages
> library(multtest)
Error in namespaceExport(ns, exports) :
  undefined exports: Surv, aareg, agreg.fit, agexact.fit, attrassign, basehaz, cch, clogit, cluster, cox.zph, coxph, coxph.control, coxph.detail, coxph.fit, coxph.wtest, <<snip>>; see above
 untangle.specials
In addition: Warning message:
S3 methods ‘[.aareg’, ‘[.Surv’, ‘[.cox.zph’, ‘[.coxph.penalty’, ‘[.ratetable’, <<snip>> ‘print.co [... truncated]
Error: package or namespace load failed for ‘multtest’
>

 

> sessionInfo()
R version 3.3.1 Patched (2016-10-18 r71535)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
[1] BiocInstaller_1.24.0 Biobase_2.34.0       BiocGenerics_0.20.0

loaded via a namespace (and not attached):
[1] Matrix_1.2-7.1  tools_3.3.1     splines_3.3.1   grid_3.3.1     
[5] lattice_0.20-34
>

 

 

multtest • 1.2k views
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Entering edit mode
Guido Hooiveld ★ 4.0k
@guido-hooiveld-2020
Last seen 6 hours ago
Wageningen University, Wageningen, the …

Sorry, problem has been solved; question can be ignored.... Sorry for this noise.

Although biocValid() did not return any problems, as a last resort I manually re-installed the dependencies of multtest, i.e. survival and MASS. After starting a new R-session, multtest now loads without any errors.... ???


 

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