Hi all,
I am trying to submit my R package to CRAN. However, I keep getting an error in
the second link, saying my package could not be installed. But the package
works perfectly fine in my personal computer. I would really appreciate it if
you could provide some possible solution.
Thanks in advance!
Best wishes,
Yuliang
________________________________________
发件人: lig...@statistik.tu-dortmund.de <lig...@statistik.tu-dortmund.de>
发送时间: 2020年2月4日 13:07
收件人: Yuliang Li
抄送: cran-submissi...@r-project.org
主题: [CRAN-pretest-archived] CRAN submission BAREB 1.0
Dear maintainer,
package BAREB_1.0.tar.gz does not pass the incoming checks automatically,
please see the following pre-tests:
Windows:
<https://win-builder.r-project.org/incoming_pretest/BAREB_1.0_20200204_031812/Windows/00check.log>
Status: 5 WARNINGs, 8 NOTEs
Debian:
<https://win-builder.r-project.org/incoming_pretest/BAREB_1.0_20200204_031812/Debian/00check.log>
Status: 1 ERROR, 1 WARNING, 2 NOTEs
Please fix all problems and resubmit a fixed version via the webform.
If you are not sure how to fix the problems shown, please ask for help on the
R-package-devel mailing list:
<https://stat.ethz.ch/mailman/listinfo/r-package-devel>
If you are fairly certain the rejection is a false positive, please reply-all
to this message and explain.
More details are given in the directory:
<https://win-builder.r-project.org/incoming_pretest/BAREB_1.0_20200204_031812/>
The files will be removed after roughly 7 days.
No strong reverse dependencies to be checked.
Best regards,
CRAN teams' auto-check service
Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64
Check: CRAN incoming feasibility, Result: NOTE
Maintainer: 'Yuliang Li <yli...@jhu.edu>'
New submission
Non-FOSS package license (Johns Hopkins University)
Possibly mis-spelled words in DESCRIPTION:
BAREB (3:8, 9:220, 9:380)
Biclustering (3:36)
DPP (9:264)
biclustering (9:35)
biclusters (9:311)
determinantal (9:235)
faciliate (9:325)
interpretability (9:349)
The Title field starts with the package name.
Size of tarball: 15969613 bytes
Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64
Check: package dependencies, Result: NOTE
Package in Depends/Imports which should probably only be in LinkingTo:
'RcppArmadillo'
Flavor: r-devel-windows-ix86+x86_64
Check: DESCRIPTION meta-information, Result: WARNING
Non-standard license specification:
Johns Hopkins University
Standardizable: FALSE
Flavor: r-devel-windows-ix86+x86_64
Check: top-level files, Result: NOTE
Non-standard files/directories found at top level:
'BAREB_1.0.pdf' 'gfortran-4.8.2-darwin13.tar.bz2'
Flavor: r-devel-windows-ix86+x86_64
Check: S3 generic/method consistency, Result: WARNING
update:
function(object, ...)
update.theta.beta:
function(theta, tau, Beta, sig)
update:
function(object, ...)
update.theta.gamma:
function(theta, tau, Gamma, S, Ds, sig)
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
Found the following apparent S3 methods exported but not registered:
update.theta.beta update.theta.gamma
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
Flavor: r-devel-windows-ix86+x86_64
Check: R code for possible problems, Result: NOTE
update.theta.beta: no visible global function definition for 'rnorm'
update.theta.beta: no visible global function definition for 'dnorm'
update.theta.beta: no visible global function definition for 'runif'
update.theta.gamma: no visible global function definition for 'rnorm'
update.theta.gamma: no visible global function definition for 'dnorm'
update.theta.gamma: no visible global function definition for 'runif'
update_RJ: no visible binding for global variable 'E'
update_RJ: no visible binding for global variable 'tau'
update_RJ: no visible binding for global variable 'm'
update_RJ: no visible binding for global variable 'T0'
update_sigma_squre: no visible global function definition for 'na.omit'
update_sigma_squre: no visible global function definition for 'rgamma'
update_w: no visible global function definition for 'rgamma'
update_w_beta: no visible global function definition for 'rgamma'
Undefined global functions or variables:
E T0 dnorm m na.omit rgamma rnorm runif tau
Consider adding
importFrom("stats", "dnorm", "na.omit", "rgamma", "rnorm", "runif")
to your NAMESPACE file.
Flavor: r-devel-windows-ix86+x86_64
Check: Rd line widths, Result: NOTE
Rd file 'updateBeta.Rd':
\usage lines wider than 90 characters:
updateBeta(X, Y, Z, delta, Beta, Gamma, E, R, S, Ds, mustar, mu, sigma,
c, C, step, runif, n, m, T0, p, q, D, theta,tau)
Rd file 'updateE.Rd':
\usage lines wider than 90 characters:
updateE( Beta, Gamma,w, X, Y, Z, delta,E, R, S, Ds, mu, mustar, sigma,
c, n, m, T0, p, q, D)
Rd file 'updateGamma.Rd':
\usage lines wider than 90 characters:
updateGamma(X, Y, Z, delta, Beta, Gamma, E, R, S, Ds, mu, mustar, sigma,
c, step, runif, n, m, T0, p, q, D, theta,tau)
Rd file 'updateR.Rd':
\usage lines wider than 90 characters:
updateR( w ,Gamma,Beta, Y, Z, delta, mu, mu_star, c, S, sigma_square,
K, E, X, m,n, q, p, T0)
Rd file 'update_w.Rd':
\examples lines wider than 100 characters:
#Suppose we know the number of patient level cluster is 2, one has 2
site level clusters and one has 3.
Rd file 'update_w_beta.Rd':
\examples lines wider than 100 characters:
#Suppose the current clustering membership indicates 3 patients in
cluster 1, 2 patients in cluster 2, 3 patinets in cluster 3, 1 patie ...
[TRUNCATED]
These lines will be truncated in the PDF manual.
Flavor: r-devel-windows-ix86+x86_64
Check: for missing documentation entries, Result: WARNING
Undocumented code objects:
'Merge' 'Merge_empty' 'Mergenomiss' 'RJi' 'RJi_empty' 'RJinomiss'
'Split' 'Split_empty' 'Splitnomiss' 'colsome' 'const' 'dmvnrm_arma'
'dmvnrm_arma0' 'getind' 'ind' 'ind1' 'likeli.theta' 'nonnan_ind'
'rmvnorm_row' 'rowsome' 'rtrun_norm' 'sample_int' 'subsome' 'ton'
'updateBetanoDPP' 'updateBetanomiss' 'updateEnomiss'
'updateGammanoDPP' 'updateGammanomiss' 'updateRi' 'updateRinomiss'
'updateRnoDPP' 'updateRnomiss'
Undocumented data sets:
'Beta0' 'Gamma0' 'X' 'Y' 'Z' 'delta' 'truth'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Flavor: r-devel-windows-ix86+x86_64
Check: compilation flags in Makevars, Result: WARNING
Variables overriding user/site settings:
CFLAGS: -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion
CXXFLAGS: -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion
Flavor: r-devel-windows-ix86+x86_64
Check: use of SHLIB_OPENMP_*FLAGS in Makefiles, Result: NOTE
src/Makevars.win: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not
in PKG_LIBS
src/Makevars.win: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking
is by C++
Use of these macros is discussed in sect 1.2.1.1 of 'Writing R
Extensions'. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for Fortran: see the manual).
Flavor: r-devel-windows-ix86+x86_64
Check: compiled code, Result: WARNING
File 'BAREB/libs/i386/BAREB.dll':
Found '_ZSt4cerr', possibly from 'std::cerr' (C++)
Object: 'truncated_normal.o'
Found '_ZSt4cout', possibly from 'std::cout' (C++)
Object: 'truncated_normal.o'
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Object: 'truncated_normal.o'
File 'BAREB/libs/x64/BAREB.dll':
Found '_ZSt4cerr', possibly from 'std::cerr' (C++)
Object: 'truncated_normal.o'
Found '_ZSt4cout', possibly from 'std::cout' (C++)
Object: 'truncated_normal.o'
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Object: 'truncated_normal.o'
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
Flavor: r-devel-windows-ix86+x86_64
Check: running examples for arch 'i386', Result: NOTE
Examples with CPU (user + system) or elapsed time > 10s
user system elapsed
update_RJ 17.5 0.65 18.18
Flavor: r-devel-windows-ix86+x86_64
Check: running examples for arch 'x64', Result: NOTE
Examples with CPU (user + system) or elapsed time > 10s
user system elapsed
update_RJ 16.12 0.08 16.21
Flavor: r-devel-linux-x86_64-debian-gcc
Check: if this is a source package, Result: WARNING
Subdirectory 'src' contains:
truncated_normal.hpp update8.o-a4f086ec
These are unlikely file names for src files.
Flavor: r-devel-linux-x86_64-debian-gcc
Check: whether package can be installed, Result: ERROR
Installation failed.
See '/srv/hornik/tmp/CRAN/BAREB.Rcheck/00install.out' for details.
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