Centos 7.8, custom-compiled R-4.1: iPath_1.0.0 won't install
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wjb2130 • 0
@339b86db
Last seen 3.0 years ago
United States

The following will not work: BiocManager::install("iPath")

Install environment includes Bioconductor version 3.14

  • These unannounced dependencies fail to install under any circumstance: gridtext, ggtext, survminer *These announced dependencies do install: mclust, BiocParallel, survival

Do you have a complete install reference for this? Centos 7.8 /7.9, compiled R-4.1. Thanks for any leads.
error iPath R compilation • 1.7k views
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Entering edit mode

You need to provide the results of your attempt to install iPath rather than simply saying the dependencies don't install. Without seeing the error messages, it's impossible for anybody to help you.

I get

> install("iPath")
Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01)
Installing package(s) 'iPath'
also installing the dependencies 'KMsurv', 'km.ci', 'gridtext', 'maxstat', 'survMisc', 'ggtext', 'survminer'

trying URL 'https://cloud.r-project.org/src/contrib/KMsurv_0.1-5.tar.gz'
Content type 'application/x-gzip' length 70896 bytes (69 KB)
==================================================
downloaded 69 KB

trying URL 'https://cloud.r-project.org/src/contrib/km.ci_0.5-2.tar.gz'
Content type 'application/x-gzip' length 29210 bytes (28 KB)
==================================================
downloaded 28 KB

trying URL 'https://cloud.r-project.org/src/contrib/gridtext_0.1.4.tar.gz'
Content type 'application/x-gzip' length 234461 bytes (228 KB)
==================================================
downloaded 228 KB

trying URL 'https://cloud.r-project.org/src/contrib/maxstat_0.7-25.tar.gz'
Content type 'application/x-gzip' length 110733 bytes (108 KB)
==================================================
downloaded 108 KB

trying URL 'https://cloud.r-project.org/src/contrib/survMisc_0.5.5.tar.gz'
Content type 'application/x-gzip' length 160581 bytes (156 KB)
==================================================
downloaded 156 KB

trying URL 'https://cloud.r-project.org/src/contrib/ggtext_0.1.1.tar.gz'
Content type 'application/x-gzip' length 1211846 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

trying URL 'https://cloud.r-project.org/src/contrib/survminer_0.4.9.tar.gz'
Content type 'application/x-gzip' length 3599577 bytes (3.4 MB)
==================================================
downloaded 3.4 MB

trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/iPath_1.0.0.tar.gz'
Content type 'application/x-gzip' length 3079193 bytes (2.9 MB)
==================================================
downloaded 2.9 MB
< snip >
*** installing help indices
** building package indices
** installing vignettes
** 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 (iPath)

> library(iPath)
Loading required package: mclust
    __  ___________    __  _____________
   /  |/  / ____/ /   / / / / ___/_  __/
  / /|_/ / /   / /   / / / /\__ \ / /   
 / /  / / /___/ /___/ /_/ /___/ // /    
/_/  /_/\____/_____/\____//____//_/    version 5.4.9
Type 'citation("mclust")' for citing this R package in publications.

Attaching package: 'mclust'

The following object is masked from 'package:htmltools':

    em

Loading required package: BiocParallel
Loading required package: survival
> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /share/apps/MKL/mkl-2019.3/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64_lin/libmkl_gf_lp64.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] iPath_1.0.0            survival_3.2-13        BiocParallel_1.28.3   
 [4] mclust_5.4.9           BiocManager_1.30.16    DBI_1.1.2             
 [7] GenomicFeatures_1.46.3 GenomicRanges_1.46.1   GenomeInfoDb_1.30.0   
[10] goseq_1.46.0           geneLenDataBase_1.30.0 BiasedUrn_1.07        
[13] htmltools_0.5.2        DT_0.20                org.Dr.eg.db_3.14.0   
[16] AnnotationDbi_1.56.2   IRanges_2.28.0         S4Vectors_0.32.3      
[19] hwriter_1.3.2          Glimma_2.4.0           tximport_1.22.0       
[22] xtable_1.8-4           BiocStyle_2.22.0       affycoretools_1.67.1  
[25] Biobase_2.54.0         BiocGenerics_0.40.0    openxlsx_4.2.5        
[28] edgeR_3.36.0           limma_3.50.0
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Entering edit mode

I hit send prematurely, so you need to look at the support site to see my actual post.

ADD REPLY •
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Entering edit mode

Thank you for response. Ì do not use "install("iPath")." I use: BiocManager::install("iPath"). Result below. There is a character limit, and I don't see an upload web function here. So this will be in 3 parts.

> BiocManager::install("iPath")
Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.0 (2021-05-18)
Installing package(s) 'iPath'
also installing the dependencies ‘gridtext’, ‘ggtext’, ‘survminer’

trying URL 'https://cloud.r-project.org/src/contrib/gridtext_0.1.4.tar.gz'
Content type 'application/x-gzip' length 234461 bytes (228 KB)
==================================================
downloaded 228 KB
trying URL 'https://cloud.r-project.org/src/contrib/ggtext_0.1.1.tar.gz'
Content type 'application/x-gzip' length 1211846 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

trying URL 'https://cloud.r-project.org/src/contrib/survminer_0.4.9.tar.gz'
Content type 'application/x-gzip' length 3599577 bytes (3.4 MB)
==================================================
downloaded 3.4 MB

trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/iPath_1.0.0.tar.gz'
Content type 'application/x-gzip' length 3079193 bytes (2.9 MB)
==================================================
downloaded 2.9 MB

begin installing package ‘gridtext’
make: *** [gridtext.ts] Error 1
make: Target `all' not remade because of errors.
* installing *source* package ‘gridtext’ ...
** package ‘gridtext’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
make[1]: Entering directory `/tmp/Rtmp2yQE6t/R.INSTALL1b063b1f99cf/gridtext/src'
g++ -std=gnu++11 -I"/centos7/R-4.1.0-x86_64/lib64/R/include" -DNDEBUG  -I'/centos7/R-
4.1.0-x86_64/lib64/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
In file included from gridtext_types.h:12:0,
                 from RcppExports.cpp:4:
grid-renderer.h: In member function ‘void GridRenderer::raster(Rcpp::RObject, Length, Length, Length, Length, bool, const GraphicsC
ontext&)’:
grid-renderer.h:61:94: error: no matching function for call to ‘Rcpp::Vector<10, Rcpp::PreserveStorage>::Vector(int, bool&, const G
raphicsContext&)’
           NumericVector(1, width), NumericVector(1, height), LogicalVector(1, interpolate, gp)
grid-renderer.h:61:94: note: candidates are:
In file included from /centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/Vector.h:52:0,
                 from /centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp.h:40,
                 from layout.h:4,
                 from gridtext_types.h:11,
                 from RcppExports.cpp:4:
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:241:5: note: Rcpp::Vector<RTYPE, S
toragePolicy>::Vector(std::initializer_list<typename Rcpp::traits::init_type<RTYPE>::type>) [with int RTYPE = 10; StoragePolicy = R
cpp::PreserveStorage; typename Rcpp::traits::init_type<RTYPE>::type = bool]
     Vector( std::initializer_list<init_type> list ) {
     ^
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:241:5: note:   candidate expects 1
 argument, 3 provided
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:233:5: note: template<class InputI
terator, class Func, class T> Rcpp::Vector<RTYPE, StoragePolicy>::Vector(InputIterator, InputIterator, Func, T, typename Rcpp::trai
ts::enable_if<Rcpp::traits::is_arithmetic<T>::value, void>::type*)
     Vector( InputIterator first, InputIterator last, Func func, T n,
     ^
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:233:5: note:   template argument d
eduction/substitution failed:
In file included from gridtext_types.h:12:0,
                 from RcppExports.cpp:4:
grid-renderer.h:61:94: note:   deduced conflicting types for parameter ‘InputIterator’ (‘int’ and ‘bool’)
           NumericVector(1, width), NumericVector(1, height), LogicalVector(1, interpolate, gp)
                                                                                              ^
In file included from /centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/Vector.h:52:0,
                 from /centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp.h:40,
                 from layout.h:4,
                 from gridtext_types.h:11,
                 from RcppExports.cpp:4:
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:226:5: note: template<class InputI
terator, class Func> Rcpp::Vector<RTYPE, StoragePolicy>::Vector(InputIterator, InputIterator, Func)
     Vector( InputIterator first, InputIterator last, Func func) {
     ^
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:226:5: note:   template argument d
eduction/substitution failed:
In file included from gridtext_types.h:12:0,
                 from RcppExports.cpp:4:
grid-renderer.h:61:94: note:   deduced conflicting types for parameter ‘InputIterator’ (‘int’ and ‘bool’)
           NumericVector(1, width), NumericVector(1, height), LogicalVector(1, interpolate, gp)
                                                                                              ^
In file included from /centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/Vector.h:52:0,
                 from /centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp.h:40,
                 from layout.h:4,
                 from gridtext_types.h:11,
                 from RcppExports.cpp:4:
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:218:5: note: template<class InputI
terator, class T> Rcpp::Vector<RTYPE, StoragePolicy>::Vector(InputIterator, InputIterator, T, typename Rcpp::traits::enable_if<Rcpp
::traits::is_arithmetic<T>::value, void>::type*)
     Vector( InputIterator first, InputIterator last, T n,
     ^
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:218:5: note:   template argument d
eduction/substitution failed:
In file included from gridtext_types.h:12:0,
                 from RcppExports.cpp:4:
grid-renderer.h:61:94: note:   deduced conflicting types for parameter ‘InputIterator’ (‘int’ and ‘bool’)
           NumericVector(1, width), NumericVector(1, height), LogicalVector(1, interpolate, gp)
                                                                                              ^
In file included from /centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/Vector.h:52:0,
                 from /centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp.h:40,
                 from layout.h:4,
                 from gridtext_types.h:11,
                 from RcppExports.cpp:4:
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:211:5: note: template<class InputI
terator> Rcpp::Vector<RTYPE, StoragePolicy>::Vector(InputIterator, InputIterator)
     Vector( InputIterator first, InputIterator last){
     ^
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:211:5: note:   template argument d
eduction/substitution failed:
In file included from gridtext_types.h:12:0,
                 from RcppExports.cpp:4:
grid-renderer.h:61:94: note:   deduced conflicting types for parameter ‘InputIterator’ (‘int’ and ‘bool’)
           NumericVector(1, width), NumericVector(1, height), LogicalVector(1, interpolate, gp)
                                                                                              ^
In file included from /centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/Vector.h:52:0,
                 from /centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp.h:40,
                 from layout.h:4,
                 from gridtext_types.h:11,
                 from RcppExports.cpp:4:
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:202:5: note: template<class T, cla
ss U1, class U2, class U3> Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const T&, Rcpp::Vector<RTYPE, StoragePolicy>::stored_type (*)
(U1, U2, U3), const U1&, const U2&, const U3&, typename Rcpp::traits::enable_if<Rcpp::traits::is_arithmetic<T>::value, void>::type*
)
     Vector( const T& siz, stored_type (*gen)(U1,U2,U3), const U1& u1, const U2& u2, const U3& u3,
     ^
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:202:5: note:   template argument d
eduction/substitution failed:
In file included from gridtext_types.h:12:0,
                 from RcppExports.cpp:4:
grid-renderer.h:61:94: note:   mismatched types ‘Rcpp::Vector<10, Rcpp::PreserveStorage>::stored_type (*)(U1, U2, U3)’ and ‘bool’
           NumericVector(1, width), NumericVector(1, height), LogicalVector(1, interpolate, gp)
                                                                                              ^
In file included from /centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/Vector.h:52:0,
                 from /centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp.h:40,
                 from layout.h:4,
                 from gridtext_types.h:11,
                 from RcppExports.cpp:4:
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:193:5: note: template<class T, cla
ss U1, class U2> Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const T&, Rcpp::Vector<RTYPE, StoragePolicy>::stored_type (*)(U1, U2),
const U1&, const U2&, typename Rcpp::traits::enable_if<Rcpp::traits::is_arithmetic<T>::value, void>::type*)
     Vector( const T& siz, stored_type (*gen)(U1,U2), const U1& u1, const U2& u2,
     ^
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Entering edit mode

Part 2 of output:

/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:193:5: note:   template argument deduction/substitution failed:
In file included from gridtext_types.h:12:0,
                 from RcppExports.cpp:4:
grid-renderer.h:61:94: note:   mismatched types ‘Rcpp::Vector<10, Rcpp::PreserveStorage>::stored_type (*)(U1, U2)’ and ‘bool’
           NumericVector(1, width), NumericVector(1, height), LogicalVector(1, interpolate, gp)
                                                                                              ^
In file included from /centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/Vector.h:52:0,
                 from /centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp.h:40,
                 from layout.h:4,
                 from gridtext_types.h:11,
                 from RcppExports.cpp:4:
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:184:5: note: template<class T, cla
ss U1> Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const T&, Rcpp::Vector<RTYPE, StoragePolicy>::stored_type (*)(U1), const U1&, typ
ename Rcpp::traits::enable_if<Rcpp::traits::is_arithmetic<T>::value, void>::type*)
     Vector( const T& siz, stored_type (*gen)(U1), const U1& u1,
     ^
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:184:5: note:   template argument d
eduction/substitution failed:
In file included from gridtext_types.h:12:0,
                 from RcppExports.cpp:4:
grid-renderer.h:61:94: note:   mismatched types ‘Rcpp::Vector<10, Rcpp::PreserveStorage>::stored_type (*)(U1)’ and ‘bool’
           NumericVector(1, width), NumericVector(1, height), LogicalVector(1, interpolate, gp)
                                                                                              ^
In file included from /centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/Vector.h:52:0,
                 from /centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp.h:40,
                 from layout.h:4,
                 from gridtext_types.h:11,
                 from RcppExports.cpp:4:
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:177:5: note: template<bool NA, class T> Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const Rcpp::sugar::SingleLogicalResult<NA, T>&)
     Vector( const sugar::SingleLogicalResult<NA,T>& obj ) {
     ^
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:177:5: note:   template argument deduction/substitution failed:
In file included from gridtext_types.h:12:0,                                                                                                               
                 from RcppExports.cpp:4:
grid-renderer.h:61:94: note:   mismatched types ‘const Rcpp::sugar::SingleLogicalResult<NA, T>’ and ‘int’
           NumericVector(1, width), NumericVector(1, height), LogicalVector(1, interpolate, gp)
                                                                                              ^
In file included from /centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/Vector.h:52:0,
                 from /centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp.h:40,
                 from layout.h:4,
                 from gridtext_types.h:11,
                 from RcppExports.cpp:4:
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:169:5: note: template<class T, class U> Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const T&, const U&, typename Rcpp::traits::enable_if<Rcpp::traits::is_arithmetic<T
>::value, void>::type*)
     Vector( const T& size, const U& u,
     ^
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:169:5: note:   template argument deduction/substitution failed:
In file included from gridtext_types.h:12:0,
                 from RcppExports.cpp:4:
grid-renderer.h:61:94: note:   mismatched types ‘typename Rcpp::traits::enable_if<Rcpp::traits::is_arithmetic<T>::value, void>::type*’ and ‘Rcpp::Vector<19>’
           NumericVector(1, width), NumericVector(1, height), LogicalVector(1, interpolate, gp)
                                                                                              ^
In file included from /centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/Vector.h:52:0,
                 from /centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp.h:40,
                 from layout.h:4,
                 from gridtext_types.h:11,
                 from RcppExports.cpp:4:
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:163:5: note: template<bool NA, class VEC> Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const Rcpp::VectorBase<RTYPE, NA_, T>&)
     Vector( const VectorBase<RTYPE,NA,VEC>& other ) {
     ^
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:163:5: note:   template argument deduction/substitution failed:
In file included from gridtext_types.h:12:0,
                 from RcppExports.cpp:4:
grid-renderer.h:61:94: note:   mismatched types ‘const Rcpp::VectorBase<10, LHS_NA, LHS_T>’ and ‘int’
           NumericVector(1, width), NumericVector(1, height), LogicalVector(1, interpolate, gp)
In file included from /centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/Vector.h:52:0,
                 from /centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp.h:40,
                 from layout.h:4,
                 from gridtext_types.h:11,
                 from RcppExports.cpp:4:
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:153:5: note: template<class U> Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const Rcpp::Dimension&, const U&)
     Vector( const Dimension& dims, const U& u) {
     ^
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:153:5: note:   template argument deduction/substitution failed:
In file included from gridtext_types.h:12:0,
                 from RcppExports.cpp:4:
grid-renderer.h:61:94: note:   candidate expects 2 arguments, 3 provided
           NumericVector(1, width), NumericVector(1, height), LogicalVector(1, interpolate, gp)
                                                                                              ^
In file included from /centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/Vector.h:52:0,
                 from /centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp.h:40,
                 from layout.h:4,
                 from gridtext_types.h:11,
                 from RcppExports.cpp:4:
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:146:5: note: template<class T> Rcp
p::Vector<RTYPE, StoragePolicy>::Vector(T, typename Rcpp::traits::enable_if<(Rcpp::traits::is_bool<T>::value && (RTYPE == 10)), voi
d>::type*)
     Vector(T value,
     ^
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:146:5: note:   template argument d
eduction/substitution failed:
In file included from gridtext_types.h:12:0,
                 from RcppExports.cpp:4:
grid-renderer.h:61:94: note:   mismatched types ‘typename Rcpp::traits::enable_if<(Rcpp::traits::is_bool<T>::value && (10 == 10)),
void>::type*’ and ‘bool’
           NumericVector(1, width), NumericVector(1, height), LogicalVector(1, interpolate, gp)
                                                                                              ^
In file included from /centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/Vector.h:52:0,
                 from /centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp.h:40,
                 from layout.h:4,
                 from gridtext_types.h:11,
                 from RcppExports.cpp:4:
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:134:5: note: Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const Rcpp::Dimension&) [with int RTYPE = 10; StoragePolicy = Rcpp::PreserveStorage]
     Vector( const Dimension& dims) {
     ^
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:134:5: note:   candidate expects 1
 argument, 3 provided
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:129:5: note: Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const int&) [with int RTYPE = 10; StoragePolicy = Rcpp::PreserveStorage]
     Vector( const int& size ) {
     ^
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:129:5: note:   candidate expects 1
 argument, 3 provided
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:123:5: note: template<class T> Rcp
p::Vector<RTYPE, StoragePolicy>::Vector(T, typename Rcpp::traits::enable_if<Rcpp::traits::is_arithmetic<T>::value, void>::type*)
     Vector(T size,
     ^
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:123:5: note:   template argument deduction/substitution failed:
In file included from gridtext_types.h:12:0,
                 from RcppExports.cpp:4:
grid-renderer.h:61:94: note:   mismatched types ‘typename Rcpp::traits::enable_if<Rcpp::traits::is_arithmetic<T>::value, void>::type*’ and ‘bool’
           NumericVector(1, width), NumericVector(1, height), LogicalVector(1, interpolate, gp)
                                                                                              ^
In file included from /centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/Vector.h:52:0,
                 from /centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp.h:40,
                 from layout.h:4,
                 from gridtext_types.h:11,
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Entering edit mode

Part 3 of failed install output:

 from RcppExports.cpp:4:
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:114:5: note: template<class T> Rcp
p::Vector<RTYPE, StoragePolicy>::Vector(const T&, Rcpp::Vector<RTYPE, StoragePolicy>::stored_type (*)(), typename Rcpp::traits::ena
ble_if<Rcpp::traits::is_arithmetic<T>::value, void>::type*)
     Vector( const T& siz, stored_type (*gen)(void),
     ^
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:114:5: note:   template argument deduction/substitution failed:
In file included from gridtext_types.h:12:0,
                 from RcppExports.cpp:4:
grid-renderer.h:61:94: note:   cannot convert ‘interpolate’ (type ‘bool’) to type ‘Rcpp::Vector<10, Rcpp::PreserveStorage>::stored_
type (*)() {aka int (*)()}’
           NumericVector(1, width), NumericVector(1, height), LogicalVector(1, interpolate, gp)
                                                                                              ^
In file included from /centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/Vector.h:52:0,
                 from /centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp.h:40,
                 from layout.h:4,
                 from gridtext_types.h:11,
                 from RcppExports.cpp:4:
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:108:5: note: Rcpp::Vector<RTYPE, S
toragePolicy>::Vector(const char*) [with int RTYPE = 10; StoragePolicy = Rcpp::PreserveStorage]
     Vector( const char* st ) {
     ^
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:108:5: note:   candidate expects 1
 argument, 3 provided
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:102:5: note: Rcpp::Vector<RTYPE, S
toragePolicy>::Vector(const string&) [with int RTYPE = 10; StoragePolicy = Rcpp::PreserveStorage; std::string = std::basic_string<c
har>]
     Vector( const std::string& st ){
     ^
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:102:5: note:   candidate expects 1
 argument, 3 provided
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:95:5: note: Rcpp::Vector<RTYPE, St
oragePolicy>::Vector(const int&, const stored_type&) [with int RTYPE = 10; StoragePolicy = Rcpp::PreserveStorage; Rcpp::Vector<RTYP
E, StoragePolicy>::stored_type = int]
     Vector( const int& size, const stored_type& u) {
     ^
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:95:5: note:   candidate expects 2
arguments, 3 provided
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:88:5: note: template<class T> Rcpp
::Vector<RTYPE, StoragePolicy>::Vector(const T&, const stored_type&, typename Rcpp::traits::enable_if<Rcpp::traits::is_arithmetic<T
>::value, void>::type*)
     Vector( const T& size, const stored_type& u,
     ^
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:88:5: note:   template argument deduction/substitution failed:
In file included from gridtext_types.h:12:0,
                 from RcppExports.cpp:4:
grid-renderer.h:61:94: note:   mismatched types ‘typename Rcpp::traits::enable_if<Rcpp::traits::is_arithmetic<T>::value, void>::typ
e*’ and ‘Rcpp::Vector<19>’
           NumericVector(1, width), NumericVector(1, height), LogicalVector(1, interpolate, gp)
                                                                                              ^
In file included from /centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/Vector.h:52:0,
                 from /centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp.h:40,
                 from layout.h:4,
                 from gridtext_types.h:11,
                 from RcppExports.cpp:4:
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:83:14: note: Rcpp::Vector<RTYPE, S
toragePolicy>::Vector(const Rcpp::no_init_vector&) [with int RTYPE = 10; StoragePolicy = Rcpp::PreserveStorage]
     explicit Vector( const no_init_vector& obj) {
              ^
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:83:14: note:   candidate expects 1
 argument, 3 provided
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:78:5: note: template<class Proxy>
Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const Rcpp::GenericProxy<Proxy>&)
     Vector( const GenericProxy<Proxy>& proxy ){
     ^
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:78:5: note:   template argument de
duction/substitution failed:
In file included from gridtext_types.h:12:0,
                 from RcppExports.cpp:4:
grid-renderer.h:61:94: note:   mismatched types ‘const Rcpp::GenericProxy<Proxy>’ and ‘int’
           NumericVector(1, width), NumericVector(1, height), LogicalVector(1, interpolate, gp)
                                                                                              ^
In file included from /centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/Vector.h:52:0,
                 from /centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp.h:40,
                 from layout.h:4,
                 from gridtext_types.h:11,
                 from RcppExports.cpp:4:
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:72:5: note: Rcpp::Vector<RTYPE, StoragePolicy>::Vector(SEXP) [with int RTYPE = 10; StoragePolicy = Rcpp::PreserveStorage; SEXP = SEXPREC*]
     Vector( SEXP x ) {
     ^
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:72:5: note:   candidate expects 1 argument, 3 provided
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:64:5: note: Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const Rcpp::Vector<RTYPE, StoragePolicy>&) [with int RTYPE = 10; StoragePolicy = Rcpp::PreserveStorage]
     Vector( const Vector& other){
     ^
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:64:5: note:   candidate expects 1 argument, 3 provided
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:56:5: note: Rcpp::Vector<RTYPE, StoragePolicy>::Vector() [with int RTYPE = 10; StoragePolicy = Rcpp::PreserveStorage]
     Vector() {
     ^
/centos7/R-4.1.0-x86_64/lib64/R/library/Rcpp/include/Rcpp/vector/Vector.h:56:5: note:   candidate expects 0 arguments, 3 provided
make[1]: *** [RcppExports.o] Error 1
make[1]: Leaving directory `/tmp/Rtmp2yQE6t/R.INSTALL1b063b1f99cf/gridtext/src'
ERROR: compilation failed for package ‘gridtext’
* removing ‘/centos7/R-4.1.0-x86_64/lib64/R/library/gridtext’
cat: ggtext.out: No such file or directory
cat: survminer.out: No such file or directory
cat: iPath.out: No such file or directory
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Entering edit mode

This might be relevant.

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Entering edit mode

Issue resolved, please close any tickets or artifacts of my post.

Steps:

  • Switch to one of the newer gcc compiler, specifically version 10.
  • rebuild R 4.1
  • re-install Bioconductor, the repeat iPath install attempt.

The listed dependencies simply couldn't be added under Centos 7.9 in-OS compiler chain. Thank you for your time.

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