3.5.1 issues?

[montge]

I'm trying to figure out if I'm missing a library that is causing a massive number of warnings (many pages of them), or whether we can ignore them. I'm using a Debian stretch based build (rocker/shiny). Many of them look like below.

g++  -I"/usr/local/lib/R/include" -DNDEBUG -I../inst/include -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppEigen/include" -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c eigs_gen.cpp -o eigs_gen.o
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:388:0,
                 from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Dense:1,
                 from /usr/local/lib/R/site-library/RcppEigen/include/RcppEigenForward.h:30,
                 from /usr/local/lib/R/site-library/RcppEigen/include/RcppEigen.h:25,
                 from eigs_gen.cpp:1:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:60:39: warning: ignoring attributes on template argument ‘__m128 {aka __vector(4) float}’ [-Wignored-attributes]
 template<> struct is_arithmetic<__m128>  { enum { value = true }; };
                                       ^
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:61:40: warning: ignoring attributes on template argument ‘__m128i {aka __vector(2) long long int}’ [-Wignored-attributes]
 template<> struct is_arithmetic<__m128i> { enum { value = true }; };
                                        ^
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:62:40: warning: ignoring attributes on template argument ‘__m128d {aka __vector(2) double}’ [-Wignored-attributes]
 template<> struct is_arithmetic<__m128d> { enum { value = true }; };
                                        ^
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:161:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f {aka __vector(4) float}’ [-Wignored-attributes]
 template<> struct unpacket_traits<Packet4f> { typedef float  type; enum {size=4, alignment=Aligned16}; typedef Packet4f half; };
                                           ^
In file included from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Core:388:0,
                 from /usr/local/lib/R/site-library/RcppEigen/include/Eigen/Dense:1,
                 from /usr/local/lib/R/site-library/RcppEigen/include/RcppEigenForward.h:30,
                 from /usr/local/lib/R/site-library/RcppEigen/include/RcppEigen.h:25,
                 from eigs_gen.cpp:1:
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:162:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d {aka __vector(2) double}’ [-Wignored-attributes]
 template<> struct unpacket_traits<Packet2d> { typedef double type; enum {size=2, alignment=Aligned16}; typedef Packet2d half; };
                                           ^
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:163:43: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4i {aka __vector(2) long long int}’ [-Wignored-attributes]
 template<> struct unpacket_traits<Packet4i> { typedef int    type; enum {size=4, alignment=Aligned16}; typedef Packet4i half; };
                                           ^
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:712:35: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f {aka __vector(4) float}’ [-Wignored-attributes]
 struct palign_impl<Offset,Packet4f>
                                   ^
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:735:35: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4i {aka __vector(2) long long int}’ [-Wignored-attributes]
 struct palign_impl<Offset,Packet4i>
                                   ^
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:758:35: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d {aka __vector(2) double}’ [-Wignored-attributes]
 struct palign_impl<Offset,Packet2d>
                                   ^
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:772:34: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4f {aka __vector(4) float}’ [-Wignored-attributes]
 ptranspose(PacketBlock<Packet4f,4>& kernel) {
                                  ^
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:777:34: warning: ignoring attributes on template argument ‘Eigen::internal::Packet2d {aka __vector(2) double}’ [-Wignored-attributes]
 ptranspose(PacketBlock<Packet2d,2>& kernel) {
                                  ^
/usr/local/lib/R/site-library/RcppEigen/include/Eigen/src/Core/arch/SSE/PacketMath.h:784:34: warning: ignoring attributes on template argument ‘Eigen::internal::Packet4i {aka __vector(2) long long int}’ [-Wignored-attributes]
 ptranspose(PacketBlock<Packet4i,4>& kernel) {
                                  ^

[eddelbuettel]

Please look up 'minimally verifiable complete example' or see eg here.

I cannot help you with a mere collation of error messages. Sorry. If it helps you, here is the page at CRAN showing it works for them on every system and we may consider them to be unbiased referees.

Lastly, no need to file the same issue twice.

[montge]

I've extracted out my example below removing some of our stuff for the minimally verifiable complete example. R dependency hell is far worse then Python, node, or java, as a lot of R packages don't use configure, autoconf, or other tools that help figure out what's missing...

Dockerfile

# Base image
FROM rocker/shiny:latest

RUN echo "deb http://ftp.debian.org/debian stretch-backports main" >> /etc/apt/sources.list.d/backports.list

RUN apt-get update -y
RUN apt-get upgrade -y

RUN export DEBIAN_FRONTEND=noninteractive
# Installing packages required for requirements.R
RUN apt-get install -y  cron \
                        git \
                        vim \
                        libssl-dev \
                        libnlopt-dev \
                        libgit2-dev \
                        libssh2-1-dev \
                        liblapack-dev \
                        libeigen3-dev \
                        libjpeg-dev \
                        libblas-dev \
                        libomp-dev \
                        build-essential \
                        libigraph0-dev \
                        libboost-all-dev \
                        libopenblas-dev \
                        libatlas-base-dev \
                        gfortran \
                        libxml2-dev \
                        libglpk-dev \
                        libgmp-dev \
                        libexplain-dev \
                        libbsd-dev \
                        tcl-dev \
                        tk-dev \
                        libxaw7-dev \
                        libgd2-xpm-dev

COPY ./rconfig/requirements.R /tmp/requirements.R
RUN Rscript /tmp/requirements.R

EXPOSE 3838

CMD ["/usr/bin/shiny-server.sh"]

below is for ./rconfig/requirements.R

if (!requireNamespace("BiocManager"))
    install.packages("BiocManager")
BiocManager::install()
BiocManager::install("graph", version = "3.8")
BiocManager::install("BiocInstaller", version = "3.8")
BiocManager::install("Rgraphviz", version = "3.8")
BiocManager::install("marray", version = "3.8")
BiocManager::install("affy", version = "3.8")
BiocManager::install("Biobase", version = "3.8")
BiocManager::install("limma", version = "3.8")
BiocManager::install("RBGL", version = "3.8")

list.of.packages <- c("ipred"
                     ,"prodlim"
                     ,"dimRed"
                     ,"ddalpha"
                     ,"recipes"
                     ,"shinyFiles"
                     ,"rhandsontable"
                     ,"shinydashboard"
                     ,"jpeg"
                     ,"leaflet"
                     ,"Rdonlp2"
                     ,"d3heatmap"
                     ,"networkD3"
                     ,"bnlearn"
                     ,"DT"
                     ,"arules"
                     ,"cleanr"
                     ,"elastic"
                     ,"elasticsearchr"
                     ,"plotly"
                     ,"rsconnect"
                     ,"ggmap"
                     ,"mapdata"
                     ,"bh"
                     ,"rcpp"
                     ,"devtools"
                     ,"dplyr"
                     ,"data.table"
                     ,"nlme"
                     ,"hexbin"
                     ,"broom"
                     ,"plyr"
                     ,"xtable"
                     ,"pbkrtest"
                     ,"caret"
                     ,"e1071"
                     ,"shinydashboard"
                     ,"shiny"
                     ,"digest"
                     ,"magrittr"
                     ,"httr"
                     ,"jsonlite"
                     ,"tibble"
                     ,"ggplot2")

new.packages <- list.of.packages[!(list.of.packages %in% installed.packages()[,"Package"])]
#if(length(new.packages)) install.packages(new.packages, repos='https://cran.rstudio.com/ 3', dependencies = TRUE)
if(length(new.packages)) install.packages(new.packages, dependencies = TRUE)


for (i.pack in 1:length(list.of.packages)){
  suppressMessages(require(list.of.packages[i.pack], character.only = TRUE, quietly = TRUE, warn.conflicts = FALSE))
}

# update.packages(checkBuilt=TRUE, ask=FALSE)
update.packages(ask = FALSE)

BTW, about that double submission, appears that was Microsoft is getting a bit too aggressive on it's new feature enabling, there was a button to enable likeness of reporting, and apparently that reset in the middle of submitting the new ticket...

[yixuan]

Hi @montge , this is a compiler warning from the Eigen library, and you can turn it off by adding the -Wno-ignored-attributes option to GCC.

[eddelbuettel]

R dependency hell is far worse then Python, node, or java,

Utter nonsense.

[eddelbuettel]

You are "wildcard installing" what will amount to a substantial portion of CRAN. In one go. Good luck with that.

For what it is worth, I have more that that installed on the machine on which I (carefully, and regularly) check reverse dependencies of Rcpp and related packages (such as RcppEigen). And this Just Works (TM).

But I have lost interest in helping you when you come to the request for a MINIMALLY complete verifiable example with a script to install several dozen packages. That's how I want to spend my unpaid volunteer time. Sorry,

[yixuan]

@montge From your log it seems that you are installing my RSpectra. To clarify, these warnings will not prevent you from building and installing RSpectra. It merely generates a huge number of warning messages.

[eddelbuettel]

I am still marveling at just how brazen this was. Starting with your list.of.packages object (which is actually a vector, but peu chere):

AP <- available.packages()
rl <- tools::package_dependencies(packages=list.of.packages,db=AP,recursive=TRUE,reverse=TRUE)
revdep <- unique(sort(do.call(c, rl)))
length(revdep)

we find that your fully resolved list of dependencies amounts to 5950 packages. Seriously?