Your names is outside a code block and so is being included as text to be formatted by LaTeX. Is that what you are seeing? Moving it inside the R code block, I don't see file names.
\documentclass{article}
\usepackage[american]{babel}
\begin{document}
<<echo=FALSE,results=tex>>=
name<-c("A.pdf","B.pdf","C.pdf","D.pdf")
for (i in 1:4) {
cat(paste("\\includegraphics[trim=0cm 10cm 0cm 5cm, clip=true, width=.7\\linewidth]{pdf_repository/",name[i],"}",sep=""),"\n")
}
@
\end{document}
gives the .tex file
\documentclass{article}
\usepackage[american]{babel}
\usepackage{Sweave}
\begin{document}
\includegraphics[trim=0cm 10cm 0cm 5cm, clip=true, width=.7\linewidth]{pdf_repository/A.pdf}
\includegraphics[trim=0cm 10cm 0cm 5cm, clip=true, width=.7\linewidth]{pdf_repository/B.pdf}
\includegraphics[trim=0cm 10cm 0cm 5cm, clip=true, width=.7\linewidth]{pdf_repository/C.pdf}
\includegraphics[trim=0cm 10cm 0cm 5cm, clip=true, width=.7\linewidth]{pdf_repository/D.pdf}
\end{document}
which compiles to a PDF with just the 4 graphics (assuming there are the 4 PDFs to include in the given directory).
pdfsuffix in line 5 again? – user1146332 Jan 22 at 10:02